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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]

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]

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]

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]

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]

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]

Porphyromonas gingivalis FimA is a major aetiological agent in periodontal disease development, however, its structure has never been determined. Here, we established the mature P. gingivalis FimA ab initio model of all six FimA variants. We determined the conserved amino acid sequences of each FimA variant and generated mature FimA models. Subsequently, we validated their quality, protein empirical distribution, and radius of gyration. Similarly, structural comparison and topological orientation were elucidated, and the probable protein–protein docking was investigated. We found that the putative mature FimA model is β-sheet-rich and, likewise, we observed that each mature FimA model has varying levels of structural differences which can be topologically subdivided into the upper, middle, and lower FimA sections. Moreover, we found that the FimA epithelial cell-binding domain (EBD) is structurally conserved within the middle FimA section of all variants and FimA–FimA docking suggests that the FimA EBDs are oriented in opposite and alternating directions of each other. [ABSTRACT FROM AUTHOR]

Abstract: Transmembrane β-barrel (TMB) proteins constitute a special class of proteins, which are located in outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. These proteins play diverse important roles in biological organisms. However, only a small number of TMB protein structures are currently known due to difficulties with experimental techniques. Hence, computational structure prediction methods based on learning are poorly tractable for these proteins. We introduce here a graph-theoretic ab initio model for predicting structures of TMB proteins by free energy minimization. TMB super-secondary structures with permuted arrangements are taken into consideration in this model. We show that finding a permuted structure is an NP-hard problem and then analyze the complexity of a tree decomposition-based algorithm to search for the optimal structure of a TMB protein corresponding to a given permutation. The robust performance of the model has been proven in our previously published results. [Copyright &y& Elsevier]

Abstract: In response to double stranded RNA (dsRNA) viruses, toll-like receptor 3 (TLR3) in fish activates signaling like human, and induces innate immunity. This suggested the existence of dsRNA binding domains in fish TLR3 as reported in higher vertebrates. In in silico analysis, leucine rich repeat (LRR) regions (4–6, 13–14, 20–22), and LRR (8–15, 17–24) were identified as key domains in rohu TLR3 as poly I:C and dsRNA of fish reovirus (AGCRV,VHSV and IHNV) binding regions. 3D-models of rohu TLR3-TIR and zebrafish TRIF were generated by homology and ab initio modeling respectively, and their interacting domains were predicted. This is the first report of TLR3 modeling in fish. [Copyright &y& Elsevier]

Abstract: As part of a continuing investigation of netrins, an emerging class of extracellular matrix proteins that are involved in axon guidance activity, we have used dynamic light scattering (DLS) and small angle X-ray scattering to investigate the solution conformation of a truncated version of netrin-4 (Δnetrin-4) that lacks the C-terminal portion. The protein is characterized by a hydrodynamic (Stokes) radius (r H ) of 4.60 (±0.20) nm, a radius of gyration (r G ) of 4.42 (±0.20) nm and a maximum particle dimension (D max ) of 16nm. More detailed ab initio modeling of the SAXS data indicates an extended rod like conformation for Δnetrin-4 in solution—a concept supported by the excellent agreement observed between experimental parameter estimates and those calculated for the ab initio models for Δnetrin-4 by the HYDROPRO program. [Copyright &y& Elsevier]

Abstract: Laminins are multidomain glycoproteins that play important roles in development and maintenance of the extracellular matrix via their numerous interactions with other proteins. Several receptors for the laminin short arms revealed their importance in network formation and intercellular signaling. However, both the detailed structure of the laminin γ-1 short arm and its organization within the complexes is poorly understood due to the complexity of the molecule and the lack of a high-resolution structure. The presented data provide the first subatomic resolution structure for the laminin γ-1 short arm in solution. This was achieved using an integrated approach that combined a number of complementary biophysical techniques such as small angle X-ray scattering (SAXS), analytical ultracentrifugation, dynamic light scattering and electron microscopy. As a result of this study, we have obtained a significantly improved model for the laminin γ-1 short arm that represents a major step forward in molecular understanding of laminin-mediated complex formations. [ABSTRACT FROM AUTHOR]

Abstract: Results concerning electronic, spatial, paramagnetic and optical properties of a self-trapped hole in NaCl are presented. The ab initio method of linear combinations of atomic orbitals (CRYSTAL code) is used. The maximum size of the supercell under consideration is 216 ions. Several types of exchange–correlation potentials (HF, B3LYP) are used. The optical transition energy is estimated from both the difference of total energies and the density of electron states. It is shown that the B3LYP40 functional provides a satisfactory description of the ground state of a defect. The energy of the πg →σu optical transition, which is unknown from experiments, is estimated theoretically. The obtained parameters of displacements of ions in the nearest neighborhood of a defect can be useful for description of magnetic characteristics of defects. [Copyright &y& Elsevier]

Abstract: There is a need to develop new, non-fluorous polymers that are highly soluble in CO2. Experimental evidence indicates that tertiary amine and pyridine groups may exhibit favorable Lewis acid–Lewis base type interactions with CO2. It is therefore reasonable to assume that incorporation of tertiary amines into the side chain or backbone of non-fluorous polymers may impart a degree of CO2-solubility to the polymer. We present experimental results for eight different tert-amine-containing polymers. Of these polymers, only propyl dimethylamine-functionalized poly(dimethylsiloxane) is soluble in CO2 at temperatures and pressures accessible in our experiments, but even this polymer is less soluble than non-functionalized poly(dimethylsiloxane) at the same chain length. We have performed ab initio calculations on tertiary amine-containing moieties representative of some of the polymers examined experimentally. Our calculations confirm that amine–CO2 interactions are indeed energetically favorable. However, we also find that the moiety self-interactions are typically more favorable than the CO2-moiety interactions. This indicates that the lack of solubility of amine-containing polymers in CO2 is a direct result of strong polymer–polymer interactions. [Copyright &y& Elsevier]

Abstract: This paper presents results of several years of experimental and theoretical work on a library of oligo(ethylene glycol)-containing self-assembled monolayers (OEG SAMs) on gold. The library consists of 15 different thiol compounds, which all contain alkyl and OEG portions of different length, as well as amide moieties forming a stabilizing lateral hydrogen bonding network. We have investigated the quality, conformation, orientation, defect structure and infrared (IR) signatures of these OEG SAMs prepared by spontaneous adsorption from dilute solutions. It is shown that solution concentration and incubation time are important factors to obtain high quality SAMs, in particular for those containing long OEG chains. Further on, the thiol compounds should contain a sufficiently long alkyl spacer to provide in plane van der Waals interactions strong enough to govern the formation of a densely packed alkylthiolate overlayer on the Au(111) surface. Such a highly ordered alkyl support, which is additionally stabilized by the lateral hydrogen bonds, enables us to vary the length of the terminal OEG portion from 1 to at least 12, without affecting the integrity and conformational characteristics of the supporting (alkyl) part of the SAM. Also, we discuss the importance of appropriate modeling tools to advance the understanding of IR signatures of the OEG SAMs. Finally, we demonstrate the generality of our “modular approach” by analyzing the structure of OEG SAMs formed by compounds extended with an additional terminal amide and an alkyl tail. Thus, the SAMs discussed herein provide an attractive platform for construction of advanced nanoarchitectures on surfaces, not only limited to biomaterials and fouling applications. [Copyright &y& Elsevier]

Abstract: Ab initio calculations are used to investigate the electronic structure and optical properties of crystalline monoclinic hafnium silicates (Hf1− x Si x O2) as a function of silicon content x (x =0, 0.25, 0.50, and 0.75). Densities of states (DOS), electronic band gaps, refractive indices and extinction coefficients of Hf1− x Si x O2 are calculated through a screened exchange (sX) method within the local density approximation (LDA). Calculational results of the DOS of Hf1− x Si x O2 indicate that these oxides are insulators. Electronic band gaps of Hf1− x Si x O2 are found to increase with increasing the silicon content. The results of optical constants of Hf1− x Si x O2 show that increasing silicon content produces a lower refractive index and a smaller extinction coefficient. The present predicted results exhibited a good agreement with the recently reported experimental observations. [Copyright &y& Elsevier]

Abstract: A novel method is proposed to derive low energy models for simple materials through ab initio optimization in space group P1 of randomly nudged cell and atom coordinates of low multiplicity supercells of the primitive cell of a hypothetical cubic model of the material with non-competitive energy and a single formula unit per primitive cell. It is shown that the number of supercells to be tried is 1, 3, 6 and 17 respectively when searching for models with 1–4 formula units per unit cell. The approach is amazingly effective for small numbers of atoms per formula unit. Application to SiNF consistently leads to new layered tetrahedral structure types with tetrahedra triply connected at N apices while singly bonded F have van der Waals interactions with neighbouring layers. The total energy of those types is ∼0.6eV lower per formula unit than currently accepted stishovite-based models. The hypothetical reaction Si3N4 +SiF4 ⇒4SiNF is then exothermic by at least 290kcal, pointing to a plausible route for the synthesis of SiNF. The creation of corresponding quantum jobs has been automated in Materials Toolkit (http://www.tothcanada.com/toolkit). [Copyright &y& Elsevier]

[Display omitted] Improvements in carbon based conductors can impact the development of a variety of new electronic and optoelectronic devices, and may offer significant weight savings (over copper), important in mass sensitive applications such as aircraft design. Published experimental work indicates that chemical doping offers the most likely route to high specific conductivity carbon-based wiring. Interpretation of the test data on potassium tetrabromoaurate, the most successful carbon nanotube dopant tested to date, is complicated by the possibility that the nominal dopant molecule and the 'in situ' configuration of the dopant species may differ, due to disassociation, ionization, or other chemical effects. Ab initio modeling of KAuBr 4 doping, in both molecular and disassociated forms, allows for the theoretical isolation of molecular, molecular fragment, and atomic dopant effects on metallic and semiconducting tubes, as a function of dopant concentration. The modeling results suggest that the dopant is most effective in a disassociated form, but that KAuBr 4 doping is not likely to produce high specific conductivity CNT wiring. [ABSTRACT FROM AUTHOR]