Sphere Encapsulated Monte Carlo: Obtaining Minimum Energy Configurations of Large Aromatic Systems.

We introduce a simple global optimization approach that is able to find minimum energy configurations of clusters containing aromatic molecules. The translational and rotational perturbations required in Monte Carlo-based methods often lead to unrealistic configurations within which two or more molecular rings intersect, causing many of the computational steps to be rejected and the optimization process to be inefficient. Here we develop a modification of the basin-hopping global optimization procedure tailored to tackle problems with intersecting molecular rings. Termed the Sphere Encapsulated Monte Carlo (SEMC) method, this method introduces sphere-based rearrangement and minimization steps at each iteration, and its performance is shown through the exploration of potential energy landscapes of polycyclic aromatic hydrocarbon (PAH) clusters, systems of interest in combustion and astrophysics research. The SEMC method provides clusters that are accurate to 5% mean difference of the minimum energy at a 10-fold speed up compared to previous work using advanced molecular dynamics simulations. Importantly, the SEMC method captures key structural characteristics and molecular size partitioning trends as measured by the molecular radial distances and coordination numbers. The advantages of the SEMC method are further highlighted in its application to previously unstudied heterogeneous PAH clusters

Hydrophobicity and Charge Distribution Effects in the Formation of Bioorganoclays

Interactions of bioorganic moieties with clay minerals have attracted attention not only from the perspective of novel bioclay materials but also because they play a crucial role in our understanding of physical and chemical processes in soils. The aim of the present article is to explore the interactions responsible for the formation of a phosphatidylcholine-kaolinite bioclay by employing a series of classical molecular dynamic simulations. Detailed analysis of the structure and energies of the resulting bioclays reveals that the phosphatidylcholine molecules bind to the kaolinite surface either via their zwitterionic heads or hydrophobic aliphatic tails, depending on the kaolinite surface characteristics and the density of organic coating. The phosphatidylcholine molecules have a tendency to form irregular layers with a preferred parallel orientation of molecules with respect to the kaolinite surface. The tails exhibit varying degrees of flexibility and disorder depending on their distance from the surface and the density of surface coating. Significant differences in the binding can be spotted with respect to the two types of kaolinite basal surfaces, i.e., the hydrophobic siloxane surface, which possesses a considerable dispersion character, and the hydrophilic alumina surface, polarized by the surface hydroxyl groups

Sphere encapsulated Monte Carlo : obtaining minimum energy configurations of large aromatic systems

We introduce a simple global optimization approach that is able to find minimum energy configurations of clusters containing aromatic molecules. The translational and rotational perturbations required in Monte Carlo-based methods often lead to unrealistic configurations within which two or more molecular rings intersect, causing many of the computational steps to be rejected and the optimization process to be inefficient. Here we develop a modification of the basin-hopping global optimization procedure tailored to tackle problems with intersecting molecular rings. Termed the Sphere Encapsulated Monte Carlo (SEMC) method, this method introduces sphere-based rearrangement and minimization steps at each iteration, and its performance is shown through the exploration of potential energy landscapes of polycyclic aromatic hydrocarbon (PAH) clusters, systems of interest in combustion and astrophysics research. The SEMC method provides clusters that are accurate to 5% mean difference of the minimum energy at a 10-fold speed up compared to previous work using advanced molecular dynamics simulations. Importantly, the SEMC method captures key structural characteristics and molecular size partitioning trends as measured by the molecular radial distances and coordination numbers. The advantages of the SEMC method are further highlighted in its application to previously unstudied heterogeneous PAH clusters.National Research Foundation (NRF)Accepted versionThis project was supported by the National Research Foundation (NRF), Prime Minister’s Office, Singapore under its Campus for Research Excellence and Technological Enterprise (CREATE) program. K.B. is grateful to the Cambridge Trust and the Stanley Studentship at King’s College, Cambridge for their financial support. M.K. gratefully acknowledges the support of the Alexander von Humboldt foundation

On the Nature of Hydrophobic Organic Compound Adsorption to Smectite Minerals Using the Example of Hexachlorobenzene-Montmorillonite Interactions

The fate of chemical pollutants in the environment is determined by various factors including the type and strength of their interactions with reactive surfaces in soils and sediments. In the present work the interactions of hexachlorobenzene (HCB) with the surface of a common clay mineral belonging to the smectite group montmorillonite (MNT) is studied by means of the density functional theory method. The MNT net surface charge, induced by isomorphic substitutions, is systematically varied and compensated by Ca2+ cations. Based on the calculated electron densities, conclusions are drawn revealing the nature of their mutual interactions, the related stability of such surface complexes as well as possible molecular arrangements. It becomes apparent that the dominant contribution to the stability of HCB-MNT complexes arises from the cation-π interactions between the HCB molecule and the nearest compensating Ca2+ cation and thus besides the MNT net surface charge the type and size of the compensating cations are expected to play a crucial role in understanding the HCB adsorption on MNT. This systematic study aims to contribute to a better mechanistic understanding of the interactions between hydrophobic organic compounds and reactive mineral surfaces

Point contact spectroscopy of superconductors via nanometer scale point contacts formed by resistive switching

Point contact spectroscopy is commonly used to investigate electronic properties of superconductors. Here we show that nanometer scale point contacts, which enable to study the superconductor properties locally, can be created by means of the resistive switching phenomenon. Our experiments were performed on sandwiched MgB2/Al/TiO2/Pt structures, where multiple bipolar resistive switching cycles were conducted. The differential conductance as a function of voltage was measured at temperatures below the critical temperature of the MgB2 superconductor. In the low-resistance state the MgB2 and Pt electrodes are connected by an ultrathin metallic filament which creates at the MgB2 electrode the Sharvin point contact with diameter below 10 nm. In this case the differential conductance data demonstrate the Andreev reflections due to the carrier transport between the superconducting MgB2 electrode and filament. From these data the two-gap superconductivity of MgB2 is clearly visible which also confirms the fit by the Blonder-Tinkham-Klapwijk model. If the bottom electrode is made of a superconductor with known gap, our approach allows us to estimate from the Andreev reflection spectrum the resistance of both the filament and point contact. We can then determine from the Sharvin formula the cross-section size of the point contact and thus also the filament cross-section size. In the high resistance state when the filament is ruptured, the differential conductance data demonstrate the spectrum typical for tunneling between two normal metals, with a zero-bias anomaly due to the Altshuler-Aronov effect. This suggests that the filament is not ruptured at the superconducting MgB2 electrode but elsewhere

A contribution of molecular modeling to supramolecular structures in soil organic matter

© 2022 The Authors. Journal of Plant Nutrition and Soil Science published by Wiley-VCH GmbHBackground: Knowledge of the stabilizing mechanisms of soil organic matter (SOM) is extremely important for numerous soil functions. For this, insight into the nature of organic matter through appropriate model concepts are crucial. Aims: For several years, a heated debate has emerged on the transformation and stabilization of SOM. In the present work, we try to contribute to this debate using molecular modeling and providing a comprehensive overview of the history of application of molecular modeling tools and developing structural concepts of SOM. Methods: Molecular modeling methods based on quantum and/or classical mechanics were used to model SOM and related properties including interactions with reactive surfaces of soil minerals. Results: Modeling of SOM aggregates revealed that hydrogen bonds and cation bridges are the main stabilizing factors in soil solution, whereas pH modifies the stability. The modeled supramolecular SOM aggregates exhibit physicochemical properties, similar to those of humic substances (HS) described in literature. The interactions of the HS models with surfaces in kaolinite nanopores led to a partial disintegration of the aggregates into individual molecules and/or smaller subaggregates. Conclusions: From the molecular modeling point of view, supramolecular microaggregate models that exhibit the properties of HS are stable in the soil solution. However, their binding to reactive mineral soil constituents can be also in the form of individual molecules or subaggregates. Thus, HS microaggregate stability is relative, depending on the interacting environment. This reconciles two points of view of HS: either as small molecules and/or supramolecular structures

Thermally induced structural evolution and age-hardening of polycrystalline V1–xMoxN (x ≈ 0.4) thin films

Rocksalt-structure (B1) (V,Mo)N alloys are inherently hard and tough ceramics. However, the mechanical properties and thermal stability of (V,Mo)N solid solutions at temperatures ⪆ 700 °C of relevance for practical applications have not been previously investigated. In this work, we synthesize single-phase B1 polycrystalline V0.57Mo0.43N0.95 coatings to investigate the effects induced by temperature on the nanostructural evolution and hardness (H) of the material. Nanoindentation measurements show that the as-deposited film (H = 23 ± 3 GPa) becomes ≈30% harder (up to 31 ± 2 GPa) upon annealing at 730 °C. Experimental characterization and analyses, based on dispersive X-ray spectroscopy, X-ray diffraction (XRD), and transmission electron microscopy (TEM), reveal that the age-hardening effect originates from decomposition of the solid solution into coherent strained cubic VN-rich/MoN-rich domains. The experimental results are complemented by the composition/temperature (V,Mo)N phase diagram – constructed upon ab initio molecular dynamics free-energies – which indicates that the separation observed in the solid solutions is of spinodal nature. Films annealed at temperatures exceeding 850 °C undergo structural coarsening, with formation of hexagonal MoxNy and cubic VN phases, which cause a decrease in hardness to ≈22 GPa. Our present findings indicate that (V,Mo)N coatings may offer outstanding mechanical performances during operation at elevated temperatures

A novel way of liver preservation improves rat liver viability upon reperfusion

Background/aim: Currently, the liver is cold-preserved at 0~4 °C for experimental and clinical purposes. Here, we investigated whether milder hypothermia during the initial phase of the preservation period was beneficial for liver viability upon reperfusion. Methods: In the first set of experiments, rat livers were preserved either conventionally in clinically used histidine-trypthopan-ketoglutarate (HTK) solution (Group A: 45 min and Group B: 24 h) or by slow cooling HTK solution (from 13 °C to 3 °C) during the initial 45 min of preservation (Group C: 24 h). In the second set of experiments, additional groups of livers were evaluated: Group BB—preservation according to Group B and Group CC—preservation according to Group C. Further, some livers were preserved at 13 °C for 24 h. Livers were then reperfused using a blood-free perfusion model. Results: Bile production was approximately 2-fold greater in Group C compared to Group B. Alanine transaminase (ALT) and aspartate transaminase (AST) release into perfusate were 2~3-fold higher in Group B compared to Group C. No significant differences were found in ALT and AST release between Group C and Group A. Livers in Group CC compared to Group BB exhibited significantly lower portal resistance, greater oxygen consumption and bromosulfophthalein excretion into bile and lower lactate dehydrogenase (LDH) release into perfusate. Histological evaluation of tissue sections in Group BB showed parenchymal dystrophy of hepatocytes, while dystrophy of hepatocytes was absent in Group CC. Livers preserved at 13 °C for 24 h exhibited severe ischemic injury. Conclusion: These results suggest that the conventional way of liver preservation is not suitable at least for rat livers and that slow cooling of HTK solution during the initial phase of cold storage can improve liver viability during reperfusion