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The infrared spectroscopic properties of selected defects involving one proton and one nearby M3+ (M = Al, Cr, Fe) substitution in orthoenstatite are investigated by first-principles calculations. Based on the theoretical results, the absorption bands experimentally observed on synthetic samples with high crystalline quality and low doping levels can be assigned to specific defect configurations. Most of them correspond to Mg vacancies at M2 sites locally compensated by one proton and one M3+ cation at a nearby M1 site. This confirms that the M3+ + H+ = 2 Mg2+ exchange mechanism is the dominant hydrogen incorporation mechanism at the lowest concentration levels in doped enstatite. At higher concentration levels, more complex incorporation mechanisms could become dominant in Al-bearing samples. [ABSTRACT FROM AUTHOR]

Single-photon emitters in hexagonal boron nitride (h-BN) exhibit compelling optical properties, such as high brightness and photostability, making them promising candidates for applications in emerging nanophotonic and quantum technologies. However, their further progress would greatly benefit from the identification of their chemical nature, which in most cases is still under debate. Among the various emitters observed in h-BN, blue quantum emitters (435 nm), also known as B-centers, are unique not only due to their promising optical properties but also because they can be fabricated at specific locations via electron-beam irradiation. Herein, ab initio calculations are used to demonstrate that the properties of a carbon chain tetramer are in excellent agreement with the characteristics of blue quantum emitters. The calculated zero-phonon line (ZPL) energy (3.13 eV) and radiative lifetime (1.62 ns) of the carbon chain tetramer align well with experimental observations. The relatively weak electron–phonon coupling indicates intense emission at the ZPL, and the Debye–Waller factor of 0.25 is consistent with experimental data. We demonstrate that, despite the absence of an inversion center in the carbon chain tetramer, it exhibits a negligible linear Stark effect, consistent with experimental findings. Additionally, our hypothesis explains the experimental observation that the formation of blue emitters is only possible in samples containing numerous ultraviolet emitters, which are probably identical to carbon dimers. [ABSTRACT FROM AUTHOR]

Proteins play crucial roles, including biocatalysis, transportation, and receptor activity, in living organisms. Moreover, their functional efficacy is influenced by their structural properties. Determining the three-dimensional structure of a protein is crucial to comprehending its catalytic mechanism, identifying potentially beneficial mutations for industrial applications, and enhancing its properties, including stability, activity, and substrate affinity. Although X-ray crystallography, nuclear magnetic resonance (NMR), and electron microscopy are employed to ascertain protein structures, many researchers have turned to bioinformatics modeling tools because of the high cost and time demands of these techniques. For structure prediction, there are three basic methods: ab initio (de novo), homology-based, and threading-based modeling techniques. In this study, 11 modeling tools belong to different approaches were compared through modeling of various proteins; Geobacillus kaustophilus ksilan alpha-1,2-glucuronidase, Actinosynnema pretiosum bifunctional cytochrome P450/NADPHP450 reductase, human high affinity cationic amino acid transporter 1 (SLC7A), human proton-coupled zinc antiporter (SLC30A) and Bacillus subtilis RNA polymerase sigma factor (sigY). Generated models were validated through QMEAN, QMEANDisCo, ProSA, ERRAT and PROCHECK tools. All of the studied proteins could be successfully modeled using homology modeling techniques, while some of the proteins could not be effectively modeled using threading or ab initio-based methods. YASARA generated reliable models for proteins that contain heteroatoms, such as P450 monooxygenases, because other tools exclude heteroatoms in their produced structures. Among approaches for modeling without templates, AlphaFold is a potent tool. On the other side, well-known template-based tools like YASARA, Robetta, and SWISS-MODEL have arisen. These results will help scientists choose the best protein modeling strategy and tool to guarantee high-quality structures. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. [ABSTRACT FROM AUTHOR]

Molecular crowding environments play a crucial role in understanding the mechanisms of biological reactions. Inside living cells, a diverse array of molecules coexists within a volume fraction ranging from 10% to 30% v/v. However, conventional spectroscopic methods often face difficulties in selectively observing the structures of particular proteins or membranes within such molecularly crowded environments due to the presence of high background signals. Therefore, it is crucial to establish in vitro measurement conditions that closely resemble the intracellular environment. Meanwhile, the neutron scattering method offers a significant advantage in selectively observing target biological components, even within crowded environments. Recently, we have demonstrated a novel scattering method capable of selectively detecting the structures of targeted proteins or membranes in a closely mimicking intracellular milieu achieved utilizing whole-cell contents (deuterated-cell debris). This method relies on the inverse contrast matching technique in neutron scattering. By employing this method, we successfully observed the fibrillization process of human amyloid beta-protein (Aβ 1–40) under a molecular crowding environment (13.1% w/v cell debris, Aβ/cell debris = ~1/25 w/w) that closely mimics the interior of living cells. Aβ protein is well known as a major pathogenic component of Alzheimer's disease. The present results combining model simulation analyses clearly show that the intracellular environment facilitates the potential formation of even more intricate higher-order aggregates of Aβ proteins than those previously reported. [ABSTRACT FROM AUTHOR]

The ADOR method of synthesizing new zeolites has yielded a range of innovative siliceous materials featuring narrow pores, which facilitate relatively strong CO2 binding. This combined experimental and computational study investigates the adsorption properties of known ADOR materials (isoreticular zeolites of the UTL family and zeolites synthesized from UOV, *CTH, IWR, and IWW parent materials), as well as hypothetical ADOR zeolites derived from UOV, IWR, and IWW. The adsorption heat of carbon dioxide on the investigated ADOR materials was ascertained through i) a series of isotherms measured at 278–318 K and ii) Monte Carlo simulations at 300 K utilizing the DFT/CC technique. Consistently higher heats of CO2 adsorption found in -D4R materials (double four-membered ring interlayer linker removed from a parent zeolite) indicate stronger dispersion interactions compared to their -S4R counterparts (single four-membered ring removed). Among ADOR zeolites, IPC-12 (UOV-D4R) was identified as a zeolite possessing the strongest CO2 binding (heat of adsorption at the zero-coverage limit of 37.3 and 37.9 kJ/mol, as determined by experiment and theory, respectively). This high adsorption energy can be attributed to a distinct structural pattern featuring an elongated shape, which effectively accommodates CO2. Comparable structural patterns to IPC-12 were also detected in as-yet hypothetical ADOR products (IWR-D4R and IWW-D4R).

We develop a theoretical model to predict the sublimation vapor pressure of pure substances. Moreover, we present a simple monoatomic molecule approximation, which reduces the complexity of the vapor pressure expression for polyatomic gaseous molecules at a convincing level of accuracy, with deviations of the Arrhenius prefactor for NaCl and NaF being 5.02% and 7.08%, respectively. The physical model is based on ab initio calculations, statistical mechanics, and thermodynamics. We illustrate the approach for Ni , Cr , Cu (metallic bond), NaCl , NaF , ZrO 2 (ionic bond) and SiO 2 (covalent bond). The results are compared against thermodynamic databases, which show high accuracy of our theoretical predictions, and the deviations of the predicted sublimation enthalpy are typically below 10%, for Cu even only 0.1%. Furthermore, the partial pressures caused by gas phase reactions are also explored, showing good agreement with experimental results. [ABSTRACT FROM AUTHOR]

The translocator protein (TSPO) is a ubiquitous transmembrane protein of great pharmacological interest thanks to its high affinity to many drug ligands. The only high-resolution 3D-structure known for mammalian TSPO was obtained by NMR for the mouse mTSPO in DPC detergent only in presence of the high-affinity PK 11195 ligand. An atomic structure of free-ligand mTSPO is still missing to better understand the interaction of ligands with mTSPO and their effects on the protein conformation. Here, we decipher the solution structures of the recombinant mTSPO without ligand both in (i) SDS, the detergent used to extract and purify the protein from E. coli inclusion bodies, and (ii) DPC, the detergent used to solve the PK 11195-binding mTSPO NMR structure. We report partially refolded and less flexible mTSPO helices in DPC compared to SDS. Besides, DPC stabilizes the tertiary structure of mTSPO, as shown by a higher intrinsic Trp fluorescence and changes in indole environment. We evaluate by SEC-MALLS that ∼135 SDS and ∼100 DPC molecules are bound to mTSPO. SEC-small-angle X-ray (SAXS) and neutron (SANS) scattering confirm a larger mTSPO-detergent complex in SDS than in DPC. Using the contrast-matching technique in SEC-SANS, we demonstrate that mTSPO conformation is more compact and less flexible in DPC than in SDS. Combining ab initio modeling with SANS, we confirm that mTSPO conformation is less elongated in DPC than in SDS. However, the free-ligand mTSPO envelope in DPC is not as compact as the PK 11195-binding protein NMR structure, the ligand stiffening the protein. [Display omitted] • mTSPO 3D-structure is partially unfolded in SDS environment. • mTSPO can refold progressively to a more native state from SDS to DPC. • mTSPO helicity and coiled coil increase from SDS to DPC environment. • Intrinsic fluorescence from mTSPO 12 Trp increases in DPC compared to SDS. • mTSPO is more compact in DPC but not as much as in presence of a stabilizing ligand. [ABSTRACT FROM AUTHOR]

Aluminum nitride (AlN) coatings have been considered for corrosion-resistant materials applicable to the aluminum (Al) industry where the AlN comes in direct contact with molten Al above 933 K. AlN coatings were synthesized by suspension plasma spray (SPS) technology using Al powder mixed with melamine suspended in hexadecane. The use of fine Al (1-5 µm) particles did not yield more than 10% AlN in the coatings. Mixing the Al powder with promotional additives such as B, BN, Mo, Y2O3, AlN, or Al4C3 solves the fine particle agglomeration and stimulates the formation of AlN in the coatings which enhances their corrosion resistance. The optimum amount of AlN promoter was 0.22 wt.% of the total suspension mass, producing up to 72% AlN in the coating as determined by Rietveld quantitative analysis (RQA) using x-ray diffraction (XRD). Another way to improve the AlN formation in the coating by post-deposition nitridation and also solve fine Al particle agglomeration is to use a wide particle size distribution of Al, with the optimum ratio being 3:1, that is, (1-5 µm):(17-35 µm). XRD analysis indicated that the coating exhibited up to 80% AlN. The coatings Vickers hardness is related to their AlN content reaching 1644 Hv (80% AlN). The coatings were tested for corrosion resistance by direct contact with molten Al-5 wt.%Mg alloy at 1123 K and found to be stable. Ab initio Born–Oppenheimer molecular dynamics (BOMD) simulation predicted these experimental results. Indeed at 1200 K, molten Al and AlN exhibit weak van der Waals interactions. The AlN(s)-Al(l) interfacial energy was calculated to be 18.2 kJ mol−1 for hexagonal AlN phase and 56.4 kJ mol−1 for cubic AlN, which means that it lies within the physisorption regime, and therefore, no reaction occurs between Al(l) and AlN(s) which confirms non-wetting application in the Al industry. [ABSTRACT FROM AUTHOR]

The subject of hydrogen–boron interactions in crystalline silicon is revisited with reference to light and elevated temperature‐induced degradation (LeTID) in boron‐doped solar silicon. Ab initio modeling of structure, binding energy, and electronic properties of complexes incorporating a substitutional boron and one or two hydrogen atoms is performed. From the calculations, it is confirmed that a BH pair is electrically inert. It is found that boron can bind two H atoms. The resulting BH2 complex is a donor with a transition level estimated at Ec–0.24 eV. Experimentally, the electrically active defects in n‐type Czochralski‐grown Si crystals co‐doped with phosphorus and boron, into which hydrogen is introduced by different methods, are investigated using junction capacitance techniques. In the deep‐level transient spectroscopy (DLTS) spectra of hydrogenated Si:P + B crystals subjected to heat‐treatments at 100 °C under reverse bias, an electron emission signal with an activation energy of ≈0.175 eV is detected. The trap is a donor with electronic properties close to those predicted for boron–dihydrogen. The donor character of BH2 suggests that it can be a very efficient recombination center of minority carriers in B‐doped p‐type Si crystals. A sequence of boron–hydrogen reactions, which can be related to the LeTID effect in Si:B is proposed. [ABSTRACT FROM AUTHOR]

Excitons, or coupled electron-hole excitations, are important both for fundamental optical properties of materials as well as and for the functionality of materials in opto-electronic devices. Depending on the material they are created in, excitons can come in many forms, from Wannier–Mott excitons in inorganic semiconductors, to molecular Frenkel or bi-molecular charge-transfer excitons in disordered organic or biological heterostructures. This multitude of materials and exciton types poses tremendous challenges for ab initio modeling. Following a brief overview of typical ab initio techniques, we summarize our recent work based on Many-Body Green’s Functions Theory in the GW approximation and Bethe–Salpeter Equation (BSE) as a method applicable to a wide range of material classes from perfect crystals to disordered materials. In particular, we emphasize the current challenges of embedding this GW-BSE method into multi-method, mixed quantum-classical (QM/MM) models for organic materials and illustrate them with examples from organic photovoltaics and fluorescence spectroscopy. Our perspectives on future studies are also presented.

Calcite is the most thermodynamically stable polymorphic phase of the CaCO3 crystal. It is widely used in modern optical instruments operating in the infrared and visible wavelengths of electromagnetic radiation. In particular, due to its anisotropic properties, calcite is used in polarization optics devices. Ab initio quantum mechanical modeling of the Raman and infrared spectra of calcite makes it possible to better understand the structure and nature of the chemical bonds of the compound, and find the optimal conditions for the effective use of unique properties of calcite in photonics tools. The calculations are performed within the framework of the density functional theory in the CRYSTAL program, using the “hybrid” B3LYP functional and the all-electronic bases of the STO-6G, PO-TZVP and BSD atomic orbitals of the Gaussian type. The obtained results for the elastic constants, Raman and infrared spectra of calcite agree satisfactorily with the available experimental data for the basic sets of POB-TZVP and BSD.

The electronic structure of Mn2+ ion substituted for the host Y atom in orthorhombic bulk YAlO3 crystals has been calculated by means of hybrid exchange-correlation functional HSE within density functional theory. The supercell approach has been used to simulate in Pbnm YAlO3 crystal the point defects, Mn-dopant and compensated the F+ center (oxygen vacancy with one trapped electron), to make unit cell neutral. Large 2 × 2 × 2 supercells of 160 atoms allow us to simulate substitutional point defect with concentration of about 3%. Mn2+ ions substituting for host Y form covalent Mn–O bonds, in opposite to the mostly ionic Y–O bond. The F center inserted to compensate the Mn2+ dopant in YAlO3 affects the electronic structure of a host material inducing three defect energy levels in the band gap. [ABSTRACT FROM AUTHOR]

Triple-negative breast cancer is the leading worldwide cause of cancer-related deaths in women. The prospection and development of new substances with antitumoral potential is of great importance for the treatment of this disease. The objective of this work was to identify a commercial drug or ligand that could potentially bind to the FZD7 transmembrane protein and inactivate the Wnt signaling pathway in triple-negative breast cancer cells. We aimed at computationally modeling the FZD7, Wnt3, and Wnt3a proteins, at making them available in protein model databases, and at conducting docking analysis to assess the binding free energy between FZD7 and the selected ligands. The Wnt3 and Wnt3a proteins were modeled by homology modeling, and the FZD7 protein was modeled by homology modeling and ab initio modeling. The ligands were selected based on their similarity to the palmitoleic acid and were gathered from the ZINC database. A total of 30 commercially available ligands were found in the ZINC database. The docking results show that the ligands zinc08221009, zinc13546050, zinc05260769, zinc04529321, and zinc05972969 are good candidates for novel drug development. The created models and conducted analysis by this work will most certainly help in future research on the Wnt signaling pathway and its components. [ABSTRACT FROM AUTHOR]

Carbon monoxide adsorption on alkali-metal exchanged chabazites (M- CHA , where M = Li, Na, K) was investigated across various Si/Al ratios. The study reveals significant insights into the adsorption behavior, including the persistence of cationic preferences with decreasing Si/Al ratios and the existence of multiple-center interactions involving alkali-metal cations and CO. Results show that for high-silica M- CHA zeolites, CO adsorption is effectively described by single and dual adsorption site models, with cation preferences varying by type. In low-silica zeolites, cation positions are primarily influenced by the aluminum distribution and Coulombic interactions. However, the propensity for single-site cation positions (Si/Al→∞) is preserved to a certain degree. The most noticeable example is the small difference between SIII' occupancies (cations in 8-membered ring windows) in Na- CHA -2 and K- CHA -2 (0.80 vs. 0.85) that strongly influences the rate of diffusion of CO in the M- CHA -2 samples. While FT-IR spectra of high-silica zeolites can be accurately described using cation site stabilities, interaction energies, and CO stretching frequencies, predicting spectra of low-silica chabazites requires a statistical approach and/or molecular dynamics simulations at the DFT level. The findings demonstrate that the dynamical behavior of adsorbates changes dramatically between different alkali metal-exchanged chabazites, highlighting the complex nature of CO adsorption at multiple Lewis acid sites. [Display omitted] • CO adsorption in M- CHA (M = Li, Na, K) zeolites across various Si/Al ratios. • High-silica M- CHA : single/dual adsorption site models explain FT-IR spectra. • Low-silica M- CHA : properties of multiple sites depend on Al distribution. • Dynamics of CO adsorption differs significantly in low-silica M- CHA samples. • Theoretical models align well with experimental spectra. [ABSTRACT FROM AUTHOR]

Low cost, scalability, potentially high energy density, and sustainability make organic magnesium (ion) battery (OMB) technologies a promising alternative to other rechargeable metal-ion battery solutions such as secondary lithium ion batteries (LIB). However, most reported OMB cathode materials have limited performance due to, in particular, low voltages often smaller than 2 V vs. Mg2+/Mg and/or low specific capacities compared to other competing battery technologies, e.g., LIB or sodium ion batteries. While the structural diversity of organic compounds and the large amount of possible chemical modifications potentially allow designing high voltage/capacity OMB electrode materials, the large search space requires efficient exploration of potential molecular-based electrode materials by rational design strategies on an atomistic scale. By means of density functional theory (DFT) calculations, we provide insights into possible strategies to increase the voltage by changes in electronic states via functionalization, by strain, and by coordination environment of Mg cations. A systematic analysis of these effects is performed on explanatory systems derived from selected prototypical building blocks: five- and six-membered rings with redox-active groups. We demonstrate that voltage increase by direct bandstructure modulation is limited, that strain on the molecular scale can in principle be used to modulate the voltage curve and that the coordination/chemical environment can play an important role to increase the voltage in OMB. We propose molecular structures that could provide voltages for Mg insertion in excess of 3 V.

The optical properties of amorphous nonstoichiometric silicon oxide (SiOx) films of variable composition (x = 0.62–1.92) formed by plasma-enhanced chemical vapor deposition are studied in the spectral range of 1.12–4.96 eV. Spectral ellipsometry showed that the refractive index dispersion character allows one to assign the formed SiOx films to silicon-like films, dielectrics, or intermediate-conductivity-type films depending on the content of oxygen in the gas phase during synthesis. A model of the SiOx structure for ab initio calculations is proposed and describes well the experimental optical spectra. Ab initio calculations of the dependences of the SiOx refractive index and band gap on stoichiometry parameter x are performed. [ABSTRACT FROM AUTHOR]

A comparison of the experimental IR absorption spectrum of the synthesized graphite oxide specimen with the calculated (using ab initio approaches) spectra of CnOmHk model systems containing the basic C54 fragment of the graphite layer and various modifying functional groups (hydroxyl, epoxy, carboxyl, and keto groups) in various numbers and combinations in the presence of a small number of solvating water molecules made it possible to clarify the nature of some signals in the medium and characteristic ranges of the IR spectrum of graphite oxide and reveal the role of hydrogen bonding between the functional groups and the water molecules. [ABSTRACT FROM AUTHOR]

Development of new functional materials for novel energy conversion and storage technologies is often assisted by ab initio modeling. Specifically, for organic materials, such as electron and hole transport materials for perovskite solar cells, LED (light emitting diodes) emitters for organic LEDs (OLEDs), and active electrode materials for organic batteries, such modeling is often done at the molecular level. Modeling of aggregate-state effects is onerous, as packing may not be known or large simulation cells may be required for amorphous materials. Yet aggregate-state effects are essential to estimate charge transport rates, and they may also have substantial effects on redox potentials (voltages) and optical properties. This paper summarizes recent studies by the author’s group of aggregation effects on the electronic properties of organic materials used in optoelectronic devices and in organic batteries. We show that in some cases it is possible to understand the mechanism and predict specific performance characteristics based on simple molecular models, while in other cases the inclusion of effects of aggregation is essential. For example, it is possible to understand the mechanism and predict the overall shape of the voltage-capacity curve for insertion-type organic battery materials, but not the absolute voltage. On the other hand, oligomeric models of p-type organic electrode materials can allow for relatively reliable estimates of voltages. Inclusion of aggregate state modeling is critically important for estimating charge transport rates in materials and interfaces used in optoelectronic devices or when intermolecular charge transfer bands are important. We highlight the use of the semi-empirical DFTB (density functional tight binding) method to simplify such calculations.

Newcastle disease virus (NDV) is an enveloped paramyxovirus. The matrix protein of the virus (M-NDV) has an innate propensity to produce virus-like particles budding from the plasma membrane of the expressing cell without recruiting other viral proteins. The virus predominantly infects the host cell via fusion with the host plasma membrane or, alternatively, can use receptor-mediated endocytic pathways. The question arises as to what are the mechanisms supporting such diversity, especially concerning the assembling and membrane binding properties of the virus protein scaffold under both neutral and acidic pH conditions. Here, we suggest a novel method of M-NDV isolation in physiological ionic strength and employ a combination of small-angle X-ray scattering, atomic force microscopy with complementary structural techniques, and membrane interaction measurements to characterize the solution behavior/structure of the protein as well as its binding to lipid membranes at pH 4.0 and pH 7.0. We demonstrate that the minimal structural unit of the protein in solution is a dimer that spontaneously assembles in a neutral milieu into hollow helical oligomers by repeating the protein tetramers. Acidic pH conditions decrease the protein oligomerization state to the individual dimers, tetramers, and octamers without changing the density of the protein layer and lipid membrane affinity, thus indicating that the endocytic pathway is a possible facilitator of NDV entry into a host cell through enhanced scaffold disintegration. [ABSTRACT FROM AUTHOR]

Abstract: A new approach is presented that allows solving optimization problems of nanosized semiconductor heterostructures. We have formulated and solved the problem of determining the optimal doping of a barrier layer consisting of a number of sublayers, which provides a preset concentration of electrons in the conduction channel of semiconductor heterostructures. To solve the problem, effective optimization algorithms based on gradient methods are developed. As an example, an Al0.25GaN/GaN heterostructure with a total barrier layer thickness of 30 nm is considered. The results obtained in the numerical experiment are consistent with the modern trend towards the transition from a homogeneous doping profile to a planar δ-doping in field-effect transistor manufacturing technologies. The developed technique of mathematical simulation and optimization can be used in field-effect transistor manufacturing technologies. The approaches presented in the work create the conditions for the automated design of such structures. [ABSTRACT FROM AUTHOR]

A quantum interatomic scattering is implemented in the direct simulation Monte Carlo (DSMC) method applied to transport phenomena in rarefied gases. In contrast to the traditional DSMC method based on the classical scattering, the proposed implementation allows us to model flows of gases over the whole temperature range beginning from 1 K up any high temperature when no ionization happens. To illustrate the new numerical approach, two helium isotopes 3 He and 4 He were considered in two canonical problems, namely, heat transfer between two planar surfaces and planar Couette flow. To solve these problems, the ab initio potential for helium is used, but the proposed technique can be used with any intermolecular potential. The problems were solved over the temperature range from 1 K to 3000 K and for two values of the rarefaction parameter δ = 1 and 10. The former corresponds to the transitional regime and the latter describes the temperature jump and velocity slip regime. No influence of the quantum effects was detected within the numerical error of 0.1% for the temperature 300 K and higher. However, the quantum approach requires less computational effort than the classical one in this temperature range. For temperatures lower than 300 K, the influence of the quantum effects exceed the numerical error and reaches 67% at the temperature of 1 K. Numerical data provided in Supplemental Material can be used to model any kind of helium flow at any temperature. [ABSTRACT FROM AUTHOR]

Abstract: Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures. To improve our understanding of the AMP structural universe we have carried out large scale ab initio 3D modeling of structurally uncharacterized AMPs that revealed similarities between predicted folds of the modeled sequences and structures of characterized AMPs. Two of the peptides whose models matched known folds are Lebocin Peptide 1A (LP1A) and Odorranain M, predicted to form β‐hairpins but, interestingly, to lack the intramolecular disulfide bonds, cation‐π or aromatic interactions that generally stabilize such AMP structures. Other examples include Ponericin Q42, Latarcin 4a, Kassinatuerin 1, Ceratotoxin D, and CPF‐B1 peptide, which have α‐helical folds, as well as mixed αβ folds of human Histatin 2 peptide and Garvicin A which are, to the best of our knowledge, the first linear αββ fold AMPs lacking intramolecular disulfide bonds. In addition to fold matches to experimentally derived structures, unique folds were also obtained, namely for Microcin M and Ipomicin. These results help in understanding the range of protein scaffolds that naturally bear antimicrobial activity and may facilitate protein design efforts towards better AMPs. [ABSTRACT FROM AUTHOR]

The 11 B/ 10 B ratio in calcite and aragonite is an important proxy of oceanic water pH. However, the physico-chemical mechanisms underpinning this approach are still poorly known. In the present study, we theoretically determine the equilibrium isotopic fractionation properties of structural boron species in calcium carbonates, BO 3 3− , BO 2 (OH) 2− and B(OH) 4 − anions substituted for carbonate groups, as well as those of B(OH) 4 − and B(OH) 3 species in vacuum. Significant variability of equilibrium isotopic fractionation properties is observed among these structural species which is related to their contrasted coordination state, B O bond lengths and atomic-scale environment. The isotopic composition of structural boron does not only depend on its coordination number but also on its medium range environment, i.e. farther than its first coordination shell. The isotopic fractionation between aqueous species and their counterparts in vacuum are assessed using previous investigations based on similar quantum-mechanical modeling approaches. At 300 K, the equilibrium isotope composition of structural trigonal species is 7–15‰ lighter than that of aqueous boric acid molecules, whereas substituted tetrahedral borate ions are heavier than their aqueous counterparts by 10–13‰. Although significant uncertainties are known to affect the theoretical prediction of fractionation factors between solids and solutions, the usually assumed lack of isotopic fractionation during borate incorporation in carbonates is challenged by these theoretical results. The present theoretical equilibrium fractionation factors between structural boron and aqueous species differ from those inferred from experiments which may indicate that isotopic equilibrium, unlike chemical equilibrium, was not reached in most experiments. Further research into the isotopic fractionation processes at the interface between calcium carbonates and aqueous solution as well as long duration experiments aimed at investigating the kinetics of equilibration of boron environment and isotopic composition are therefore required to refine our understanding of boron coprecipitation in carbonates and thus the theory behind the use of boron isotopes as an ocean pH proxy. [ABSTRACT FROM AUTHOR]

Rational design of active electrode materials is important for the development of advanced lithium and post-lithium batteries. Ab initio modeling can provide mechanistic understanding of the performance of prospective materials and guide design. We review our recent comparative ab initio studies of lithium, sodium, potassium, magnesium, and aluminum interactions with different phases of several actively experimentally studied electrode materials, including monoelemental materials carbon, silicon, tin, and germanium, oxides TiO2 and VxOy as well as sulphur-based spinels MS2 (M = transition metal). These studies are unique in that they provided reliable comparisons, i.e., at the same level of theory and using the same computational parameters, among different materials and among Li, Na, K, Mg, and Al. Specifically, insertion energetics (related to the electrode voltage) and diffusion barriers (related to rate capability), as well as phononic effects, are compared. These studies facilitate identification of phases most suitable as anode or cathode for different types of batteries. We highlight the possibility of increasing the voltage, or enabling electrochemical activity, by amorphization and p-doping, of rational choice of phases of oxides to maximize the insertion potential of Li, Na, K, Mg, Al, as well as of rational choice of the optimum sulfur-based spinel for Mg and Al insertion, based on ab initio calculations. Some methodological issues are also addressed, including construction of effective localized basis sets, applications of Hubbard correction, generation of amorphous structures, and the use of a posteriori dispersion corrections. [ABSTRACT FROM AUTHOR]

Single-phase concentrated solid solution alloys, including high entropy alloys, exhibit remarkable mechanical properties as well as extraordinary corrosion and radiation resistance compared to pure metals and dilute alloys. However, the mechanisms responsible for these properties are unknown in many cases. In this work, we employ ab initio molecular dynamics based on density functional theory to study the diffusion of interstitial atoms in Ni and Ni-based face-centered cubic concentrated alloys including NiFe, NiCo and NiCoCr. We model the defect trajectories over 100 ps and estimate the tracer diffusion coefficients, correlation factors and activation energies. We find that the diffusion mass transport in concentrated alloys is not only slower than that in pure components, i.e. sluggish diffusion, but also chemically non-homogeneous. The results obtained here can be used to understand and predict atomic segregation and phase separation in concentrated solid solution alloys under irradiation. [ABSTRACT FROM AUTHOR]

Aluminum-silicon is a simple binary eutectic system with limited solid solubility of aluminum in silicon. Hypoeutectic compositions of Al-Si are the basis of several alloys for aerospace and automotive industries. The eutectic phase mixture contains coarse plate-like silicon. Typically, alkaline earth elements such as strontium, calcium, and barium are added in minute quantities that produce a fibrous network of silicon to improve the fracture toughness. Here, we use first-principles calculations to understand the origin of these morphological variations and explain these through interatomic interactions between aluminum, silicon, and inoculant atoms. Our results show that silicon atoms cluster together and arrange themselves in a planar (100) configuration within the aluminum matrix. When strontium, calcium, or barium atoms are added to the system, these atoms prefer to be near the silicon clusters and change the planar morphology to a three-dimensional configuration with facets on (111) planes. [Display omitted] [ABSTRACT FROM AUTHOR]

The ADOR method of synthesizing new zeolites has yielded a range of innovative siliceous materials featuring narrow pores, which facilitate relatively strong CO 2 binding. This combined experimental and computational study investigates the adsorption properties of known ADOR materials (isoreticular zeolites of the UTL family and zeolites synthesized from UOV , *CTH , IWR , and IWW parent materials), as well as hypothetical ADOR zeolites derived from UOV , IWR , and IWW. The adsorption heat of carbon dioxide on the investigated ADOR materials was ascertained through i) a series of isotherms measured at 278–318 K and ii) Monte Carlo simulations at 300 K utilizing the DFT/CC technique. Consistently higher heats of CO 2 adsorption found in -D4R materials (double four-membered ring interlayer linker removed from a parent zeolite) indicate stronger dispersion interactions compared to their -S4R counterparts (single four-membered ring removed). Among ADOR zeolites, IPC-12 (UOV -D4R) was identified as a zeolite possessing the strongest CO 2 binding (heat of adsorption at the zero-coverage limit of 37.3 and 37.9 kJ/mol, as determined by experiment and theory, respectively). This high adsorption energy can be attributed to a distinct structural pattern featuring an elongated shape, which effectively accommodates CO 2. Comparable structural patterns to IPC-12 were also detected in as-yet hypothetical ADOR products (IWR -D4R and IWW -D4R). • ADOR zeolites characterized using XRD, Ar physisorption, SEM, and EDX analysis. • Type I isotherms observed for CO 2 adsorption in zeolites at various temperatures. • Isosteric heat calculated using the Clausius-Clapeyron expression. • Heat of adsorption relates to framework density and local adsorption site environment. • IPC-12 exhibits anomalously strong CO 2 adsorption due to a unique structural motif. [ABSTRACT FROM AUTHOR]

Background: Designing drug molecules targeting biotin carboxyl carrier protein of acetyl-CoA carboxylase (AccB), a novel common drug target among the pathogens of infective endocarditis (IE), would be imperative for IE therapy. Methods: Homology modelling of AccB was performed in complex with biotin using Modeller9v8. DOPE score, PROCHECK, ProSA and ProQ analyses were used for model validation. Allosteric site residues of AccB were determined using PyMOL. The structural analogs of biotin were searched from the Ligand.Info metadatabase tool to compile an in-house library. Structure-based virtual screening for AccB was performed using Maestro v9.2. Molecular dynamic (MD) simulations for AccB - lead1 docking complex were performed using Desmond v3.0. Results: The AccB structure was evaluated as reliable one for docking analysis. The prepared in-house library comprised of 357 biotin analogs. The structure-based virtual screening on AccB and in-house library led to identification of two lead molecules with better binding affinity compared to biotin (XP Gscore -2.216 kcal/mol). Lead1 showed the lowest XP Gscore of -5.847 kcal/mol with strong hydrogen bond network and good van der Waal interactions with AccB. Stable nature of the docking interactions was reproduced through MD simulations after 10 ns. Interpretation: The binding orientations of lead1 were well in agreement with binding orientations of existing inhibitors. MD simulations shed light on natural dynamics of the docking complex in solution on different timescales. Conclusions: Lead1 could, therefore, be considered for designing potent inhibitor of infective endocarditis.

The widespread use of nanofiltration and electrodialysis membrane processes is slowed down by the difficulties in predicting the membrane performances for treating streams of variable ionic compositions. Correlations between ion hydration properties and solute transfer can help to overcome this drawback. This research aims to investigate the correlation between theoretically evaluated hydration properties of major ions in solution and experimental values of neutral organic solute fluxes. In particular, ion hydration energies, coordination and hydration number and the average ion-water distance of Na+, Ca2+, Mg2+, Cl− and SO42− were calculated at a high quantum mechanics level and compared with experimental sugar fluxes previously reported. The properties computed by simple and not computationally expensive models were validated with information from the literature. This work discusses the correlation between the hydration energies of ions and fluxes of three saccharides, measured through nanofiltration and ionic-exchange membranes. In nanofiltration, the sugar flux increases with the presence of ions of increasing hydration energy. Instead, inverse linear correlations were found between the hydration energy and the sugar fluxes through ion exchange membranes. Finally, an empirical model is proposed for a rough evaluation of the variation in sugar fluxes as function of hydration energy for the ion exchange membranes in diffusion experiments.

Experimental investigations have shown that the presence of electrolytes has a strong influence on the transfer of neutral organic solutes through ion exchange membranes used in electrodialysis. It was further demonstrated that this influence is due to the impact of the membrane counter-ions on the noncovalent interactions existing between the hydrated and charged polymer chains in the membrane. The aim of this work is to investigate the structural properties of hydrated CMX membranes equilibrated with different counter-ions. Different methods, such as Infrared spectra (IR), contact angle and Differential Scanning Calorimetry (DSC) measurements, were used to characterize the membrane samples soaked in different electrolytes. In addition, IR spectra were calculated using a quantum mechanics approach and compared with the experimental ones. Shifts of characteristic IR peaks as function of membrane ionic form were observed in both experimental and computed spectra. Both spectra present shifts to lower wavenumber in presence of cations with higher hydration number. The contact angle of CMX membranes also increases in presence of more hydrated ions revealing a decrease of the hydrophilicity of the membrane. Concerning DSC, the freezing temperature of the water entrapped in the membrane polymeric network soaked with different electrolytes was measured. A shift at lower temperature was found for more hydrated trapped ions. The computational and experimental membrane structural properties were correlated with the corresponding transfer properties (sugar fluxes) and a good agreement was obtained. [ABSTRACT FROM AUTHOR]

Despite the importance of boron as a proxy of past ocean pH, the crystal-chemical factors controlling its incorporation in the structure of calcium carbonates are still poorly understood. This is partly linked to an imperfect knowledge of the coordination, protonation state and local environment of boron species in these minerals. In the present study, we use first-principles quantum mechanical tools to model selected trigonal and tetragonal boron species in calcite and aragonite. The stable geometry of the models is obtained from standard energy minimization schemes or using a more advanced metadynamics exploration of their configurational space. The computation of 11 B NMR chemical shifts and quadrupolar coupling parameters enables a straightforward comparison of the models to existing experimental NMR data. The results show that B in calcium carbonates does occur as structural species substituted for CO 3 2− anions. The B speciation depends on the polymorph considered. In calcite, structural boron is present as partially deprotonated trigonal BO 2 (OH) 2− species coexisting with a fraction of substituted B(OH) 4 − groups. In aragonite, the B(OH) 4 − substitution for CO 3 2− anions is dominant. Different species, including entrapped B(OH) 3 molecules and substituted BO 3 3− groups also occur in biogenic samples. The diversity of B speciation reflects a diversity of B incorporation mechanisms and sheds light on previous studies confronting B isotopic composition determination with NMR observations. The mechanisms of boron incorporation in calcium carbonates are probably more complex than usually assumed in the literature using boron isotopes as a proxy of paleo-atmospheric CO 2 reconstructions. Although not invalidating the empirical paleo-pH proxy, these results call for a better understanding of the fundamental mechanisms of boron incorporation in carbonates. [ABSTRACT FROM AUTHOR]

Density functional theory (DFT)-based ab initio methods become standard research tools in various research fields, including nuclear materials science. However, having strongly correlated f -electrons, lanthanide- and actinide-bearing nuclear materials are computationally challenging for DFT methods and straightforward DFT calculations of these materials can easily produce false results. In this contribution we benchmark the DFT + U method, with the Hubbard U parameter derived ab initio , for prediction of structural and thermochemical parameters of nuclear materials, including various actinide-bearing molecular complexes and lanthanide-bearing monazite- and xenotime-type prospective ceramic nuclear waste host forms. Our studies show that the applied DFT + U method improves significantly prediction of DFT by producing results with uncertainties similar to those of the higher order, but computationally unfeasible ab initio methods, and the experimental data, and thus allows for reliable and feasible ab initio computation of even chemically complex nuclear materials. [ABSTRACT FROM AUTHOR]

Concurrent multiscale coupling is a powerful tool for obtaining quantum mechanically (QM) accurate material behavior in a small domain while still capturing long range stress fields using a molecular mechanical (MM) description. We outline an improved scheme for QM/MM coupling in metals which permits the QM treatment of a small region chosen from a large, arbitrary MM domain to calculate total system energy and relaxed geometry. In order to test our improved method, we compute solute–vacancy binding in bulk Al as well as the binding of Mg and Pb to a symmetric Σ 5 grain boundary. Results are calculated with and without our improvement to the QM/MM scheme and compared to periodic QM results for the same systems. We find that our scheme accurately and efficiently reproduces periodic QM target values in these test systems and therefore can be expected to perform well using more general geometries. [ABSTRACT FROM AUTHOR]

A fundamental understanding of the transition metal dichalcogenide (TMDC)-metal interface is critical for their utilization in a broad range of applications. We investigate how the deposition of palladium (Pd), as a model metal, on WTe 2 (001), leads to the assembly of Pd into clusters and nanoparticles. Using X-ray photoemission spectroscopy, scanning tunneling microscopy imaging, and ab initio simulations, we find that Pd nucleation is driven by the interaction with and the availability of mobile excess tellurium (Te) leading to the formation of Pd-Te clusters at room temperature. Surprisingly, the nucleation of Pd-Te clusters is not affected by intrinsic surface defects, even at elevated temperatures. Upon annealing, the Pd-Te nanoclusters adopt an identical nanostructure and are stable up to ∼523 K. Density functional theory calculations provide a foundation for our understanding of the mobility of Pd and Te atoms, preferential nucleation of Pd-Te clusters, and the origin of their annealing-induced monodispersity. These results highlight the role the excess chalcogenide atoms may play in the metal deposition process. More broadly, the discoveries of synthetic pathways yielding thermally robust monodispersed nanostructures on TMDCs are critical to the manufacturing of novel quantum and microelectronics devices and catalytically active nano-alloy centers., (© The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences.)