Se Nanopowder Conversion into Lubricious 2D Selenide Layers by Tribochemical Reactions.

Transition metal dichalcogenide (TMD) coatings have attracted enormous scientific and industrial interest due to their outstanding tribological behavior. The paradigmatic example is MoS2 , even though selenides and tellurides have demonstrated superior tribological properties. Here, an innovative in operando conversion of Se nanopowders into lubricious 2D selenides, by sprinkling them onto sliding metallic surfaces coated with Mo and W thin films, is described. Advanced material characterization confirms the tribochemical formation of a thin tribofilm containing selenides, reducing the coefficient of friction down to below 0.1 in ambient air, levels typically reached using fully formulated oils. Ab initio molecular dynamics simulations under tribological conditions reveal the atomistic mechanisms that result in the shear-induced synthesis of selenide monolayers from nanopowders. The use of Se nanopowder provides thermal stability and prevents outgassing in vacuum environments. Additionally, the high reactivity of the Se nanopowder with the transition metal coating in the conditions prevailing in the contact interface yields highly reproducible results, making it particularly suitable for the replenishment of sliding components with solid lubricants, avoiding the long-lasting problem of TMD-lubricity degradation caused by environmental molecules. The suggested straightforward approach demonstrates an unconventional and smart way to synthesize TMDs in operando and exploit their friction- and wear-reducing impact.

Nanoscale MXene Interlayer and Substrate Adhesion for Lubrication: A Density Functional Theory Study.

Understanding the interlayer interaction at the nanoscale in two-dimensional (2D) transition metal carbides and nitrides (MXenes) is important to improve their exfoliation/delamination process and application in (nano)-tribology. The layer-substrate interaction is also essential in (nano)-tribology as effective solid lubricants should be resistant against peeling-off during rubbing. Previous computational studies considered MXenes' interlayer coupling with oversimplified, homogeneous terminations while neglecting the interaction with underlying substrates. In our study, Ti-based MXenes with both homogeneous and mixed terminations are modeled using density functional theory (DFT). An ad hoc modified dispersion correction scheme is used, capable of reproducing the results obtained from a higher level of theory. The nature of the interlayer interactions, comprising van der Waals, dipole-dipole, and hydrogen bonding, is discussed along with the effects of MXene sheet's thickness and C/N ratio. Our results demonstrate that terminations play a major role in regulating MXenes' interlayer and substrate adhesion to iron and iron oxide and, therefore, lubrication, which is also affected by an external load. Using graphene and MoS2 as established references, we verify that MXenes' tribological performance as solid lubricants can be significantly improved by avoiding -OH and -F terminations, which can be done by controlling terminations via post-synthesis processing.

Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region.

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.

Balancing Cost and Accuracy in Quantum Mechanical Simulations on Collagen Protein Models.

Collagen proteins are spread in almost every vertebrate's tissue with mechanical function. The defining feature of this fundamental family of proteins is its well-known collagen triple-helical domain. This helical domain can have different geometries, varying in helical elongation and interstrands contact, as a function of the amino acidic composition. The helical geometrical features play an important role in the interaction of the collagen protein with cell receptors, but for the vast majority of collagen compositions, these geometrical features are unknown. Quantum mechanical (QM) simulations based on the density functional theory (DFT) provide a robust approach to characterize the scenario on the collagen composition-structure relationships. In this work, we analyze the role of the adopted computational method in predicting the collagen structure for two purposes. First, we look for a cost-effective computational approach to apply to a large-scale composition-structure analysis. Second, we attempt to assess the robustness of the predictions by varying the QM methods. Therefore, we have run geometry optimization on periodic models of the collagen protein using a variety of approaches based on the most commonly used DFT functionals (PBE, HSE06, and B3LYP) with and without dispersion correction (D3ABC). We have coupled these methods with several different basis sets, looking for the highest accuracy/cost ratio. Furthermore, we have studied the performance of the composite HF-3c method and the semiempirical GFN1-xTB method. Our results identify a computational recipe that is potentially capable of predicting collagen structural features in line with DFT simulations, with orders of magnitude reduced computational cost, encouraging further investigations on the topic.

Structure and Reactivity of Oxygen-Bridged Diamino Dicopper(II) Complexes in Cu-Ion-Exchanged Chabazite Catalyst for NH3-Mediated Selective Catalytic Reduction.

The NH3-mediated selective catalytic reduction (NH3-SCR) of NOx over Cu-ion-exchanged chabazite (Cu-CHA) catalysts is the basis of the technology for abatement of NOx from diesel vehicles. A crucial step in this reaction is the activation of oxygen. Under conditions for low-temperature NH3-SCR, oxygen only reacts with CuI ions, which are present as mobile CuI diamine complexes [CuI(NH3)2]+. To determine the structure and reactivity of the species formed by oxidation of these CuI diamine complexes with oxygen at 200 °C, we have followed this reaction, using a Cu-CHA catalyst with a Si/Al ratio of 15 and 2.6 wt% Cu, by X-ray absorption spectroscopies (XANES and EXAFS) and diffuse reflectance UV-Vis spectroscopy, with the support of DFT calculations and advanced EXAFS wavelet transform analysis. The results provide unprecedented direct evidence for the formation of a [Cu2(NH3)4O2]2+ mobile complex with a side-on µ-η2,η2-peroxo diamino dicopper(II) structure, accounting for 80-90% of the total Cu content. These [Cu2(NH3)4O2]2+ are completely reduced to [CuI(NH3)2]+ at 200 °C in a mixture of NO and NH3. Some N2 is formed as well, which suggests the role of the dimeric complexes in the low-temperature NH3-SCR reaction. The reaction of [Cu2(NH3)4O2]2+ complexes with NH3 leads to a partial reduction of the Cu without any formation of N2. The reaction with NO results in an almost complete reduction to CuI, under the formation of N2. This indicates that the low-temperature NH3-SCR reaction proceeds via a reaction of these complexes with NO.

Exfoliation Energy of Layered Materials by DFT-D: Beware of Dispersion!

In this work, we have computed the exfoliation energy (the energy required to separate a single layer from the bulk structure), the interlayer distance, and the thermodynamic state functions for representative layered inorganic minerals such as Brucite, Portlandite, and Kaolinite, while leaving the more classical 2D transition-metal dichalcogenides (like MoS2) for future work. Such materials are interesting for several applications in the field of adsorption and in prebiotic chemistry. Their peculiar features are directly controlled by the exfoliation energy. In materials without cations/anions linking different layers, the interactions keeping the layers together are of weak nature, mainly dispersion London interactions and hydrogen bonds, somehow challenging to deal with computationally. We used Hartree-Fock (HF) and density functional theory (DFT) approaches focusing on the role of dispersion forces using the popular and widespread Grimme's pairwise dispersion schemes (-D2 and -D3) and, as a reference method, the periodic MP2 approach based on localized orbitals (LMP2). The results are highly dependent on the choice of the scheme adopted to account for dispersion interactions. D2 and D3 schemes combined with either HF or DFT lead to overestimated exfoliation energies (about 2.5 and 1.7 times higher than LMP2 data for Brucite/Portlandite and Kaolinite) and underestimated interlayer distances (by about 3.5% for Brucite/Portlandite). The reason is that D2 and D3 corrections are based on neutral atomic parameters for each chemical element which, instead, behave as cations in the considered layered material (Mg, Ca, and Al), causing overattractive interaction between layers. More sophisticated dispersion corrections methods, like those based on nonlocal vdW functionals, many body dispersion model, and exchange-hole dipole moment not relying on atom-typing, are, in principle, better suited to describe the London interaction of ionic species. Nonetheless, we demonstrate that good results can be achieved also within the simpler D2 and D3 schemes, in agreement with previous literature suggestions, by adopting the dispersion coefficients of the preceding noble gas for the ionic species, leading to energetics in good agreement with LMP2 and structures closer to the experiments.

Elucidating the Nature of Interactions in Collagen Triple-Helix Wrapping.

Collagen is the most abundant protein family in the animal kingdom. Its structural motif envisages three polypeptide chains coiled in the so-called collagen triple helix. Depending on the triplet amino acid sequence of the chains, collagen has different helical arrangements. Such atomic-scale structural variations have a large impact on the large-scale structure of collagen. In this Letter, we elucidate the interactions that are responsible for a specific helical pattern of the collagen protein by means of DFT-D-based computer simulations. We demonstrate that interchain interactions and solvation effects stabilize compact helices over elongated ones. Conversely, elongated helices are stabilized by less geometrical strain and entropic factors. Our computational procedure predicts the collagen helical pattern in agreement with the experimental evidence.

Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites.

Several computational techniques for solid-state applications have recently been proposed to enlarge the scope of computer simulations of large molecular systems. In this contribution, we focused on two of these, namely, HF-3c and PBEh-3c. They were recently proposed by the Grimme's group, as "low-cost" ab initio-based techniques for electronic structure calculation of large systems and were proved to be effective essentially for organic molecules. HF-3c is based on a Hartree-Fock Hamiltonian with a minimal Gaussian quality basis set, whereas PBEh-3c is a density functional theory (DFT) based method with a hybrid functional and a medium-quality basis set. Both HF-3c and PBEh-3c account for dispersion (London) interactions and are free from the basis set superposition error due to limited basis set size, through several pairwise semiempirical corrections. To the best of our knowledge, despite the promising results on the cost-accuracy side of molecular simulations of organic molecules, these methods have been used only in few cases for solid-state applications. In this contribution, we studied the performance of HF-3c and PBEh-3c for predicting the properties of inorganic crystals to enlarge the applicability of these cheap and fast methodologies. As a testing ground, we have chosen a well-known class of material, e.g., microporous all-silica zeolites. We benchmarked geometries, formation energies, vibrational features, and mechanical properties by comparing the results with literature data from both experiment and computer simulation. For structures, HF-3c is extremely accurate in predicting the zeolites cell volume, albeit we do not include any vibrational contribution, neither zero point nor thermal, on the computed volumes, which may introduce small variations in the predicted values. For the energetic, the relative stability of the zeolites using the DFT//HF-3c approach allows predictions within the experimental error for most of the cases taken into consideration when the experimental enthalpies were corrected back to electronic energies by using the HF-3c thermodynamic contributions computed in the harmonic approximation. This strategy is particularly convenient, as the slow step (geometry optimization) is carried out with the cheapest HF-3c method, whereas the fast step (single point energy evaluation) is carried out with costly DFT methods. In this sense, the use of the DFT//HF-3c approach results to be a promising one to predict the stability and structure of microporous materials. Finally, the HF-3c method predicts the mechanical properties of the zeolite set in reasonable agreement with respect to those computed with the state-of-the-art DFT simulations, indicating the HF-3c method as a possible technique for the mechanical stability screenings of microporous materials.

Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations.

Collagen is a protein family defined by a triple helix motif, which comprises roughly one-third of the total human protein content. Decoding the reasons underlying the stability of the collagen triple helix is of both fundamental and applicative relevance, for instance, to guide collagen protein engineering. In principle, full quantum mechanical approaches based on density functional theory (DFT) are ideal to study the subtle physicochemical features of collagen. Unfortunately, the huge size of the protein prevents the straightforward application of DFT to realistic collagen protein models. In this paper, we propose a new realistic model of the collagen protein based on a periodic approach. The protein model exploits the intrinsic symmetry of the collagen triple helix, dramatically lowering the cost of the simulations. This allows using accurate hybrid DFT simulations (B3LYP-D/TZP) for systematic studies of the collagen protein features. We have tested the proposed model/level-of-theory combination to analyze the well-known proline-conformation/collagen-stability relationship. For this purpose, we have performed an extensive conformational analysis of the proline ring within the protein, clarifying some of the reasons linking specific ring conformations to helix positions. Throughout our data analysis, we have also obtained "for free" the collagen interstrand binding energy. Simulation results demonstrate that London dispersion interactions play a dominant role in the whole helix stability. The good agreement with the experimental data validates the use of the proposed model/level of theory to assist the active field of collagen-like peptide synthesis.

Method Dependence of Proline Ring Flexibility in the Poly-l-Proline Type II Polymer.

We studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered heterocycle pyrrolidine ring for the above models, dictating the collagen main features. We also compared the DFT-D results with those from the recently proposed cost-effective HF-3c method and our variant HF-3c-027, both based on Hartree-Fock Hamiltonian and Gaussian minimal basis set properly corrected for basis set superposition error, structure deficiencies, and dispersion interactions. We found that dispersion interactions are essential to destabilize specific conformers. While the HF-3c and its HF-3c-027 variant are unreliable to predict accurately the energy of the ring conformers, structures are accurate. Indeed, the cost-effective DFT-D//HF-3c-027 approach in which the energetic is from the accurate DFT-D method on HF-3c-027 structures provides energetic in line with that derived by the costly DFT-D//DFT-D approach, paving the way to simulate more realistic collagen models of much larger size. The adoption of either PBE or B3LYP functional for the electronic part of the DFT-D method gives very similar results, recommending the first as the most cost-effective method for simulating large collagen models. The predicted most stable conformation computed for the periodic poly proline (type II) model allows for a higher flexibility, in agreement with experimental studies on collagen protein. The present results open the way to large-scale calculations of the collagen/hydroxyapatite system, crucial for understanding the atomistic details in bones and teeth.

Assessment of Different Quantum Mechanical Methods for the Prediction of Structure and Cohesive Energy of Molecular Crystals.

A comparative assessment of the accuracy of different quantum mechanical methods for evaluating the structure and the cohesive energy of molecular crystals is presented. In particular, we evaluate the performance of the semiempirical HF-3c method in comparison with the B3LYP-D* and the Local MP2 (LMP2) methods by means of a fully periodic approach. Three benchmark sets have been investigated: X23, G60, and the new K7; for a total of 82 molecular crystals. The original HF-3c method performs well but shows a tendency at overbinding molecular crystals, in particular for weakly bounded systems. For the X23 set, the mean absolute error for the cohesive energies computed with the HF-3c method is comparable to the LMP2 one. A refinement of the HF-3c has been attempted by tuning the dispersion term in the HF-3c energy. While the performance on cohesive energy prediction slightly worsens, optimized unit cell volumes are in excellent agreement with experiment. Overall, the B3LYP-D* method combined with a TZP basis set gives the best results. For cost-effective calculations on molecular crystals, we propose to compute cohesive energies at the B3LYP-D*/TZP level of theory on the dispersion-scaled HF-3c optimized geometries (i.e., B3LYP-D*/TZP//HF-3c(0.27) also dubbed as SP-B3LYP-D*). Besides, for further benchmarking on molecular crystals, we propose to combine the three test sets in a new one denoted as MC82.