Terms Of Free Energy Research Articles

Improving the anti-autolytic ability of alkaline protease from Bacillus alcalophilus by a rationally combined strategy.

Detergent enzymes have been extensively developed as eco-friendly alternatives to harmful chemicals, with alkaline protease representing a significant portion of detergent enzyme sales. However, the self-cleavage function of alkaline protease impacts its activity and overall application. Therefore, a new rational combinatorial strategy is proposed based on self-molecular docking (Self-ZDOCK) and molecular dynamics (MD) simulations. Self-ZDOCK is a computational method for predicting the binding mode of proteins to themselves, which is crucial for understanding the self-cleavage mechanism of proteases. On the other hand, MD simulation is a powerful tool to gain insight into the dynamic behaviour of proteins over time, and thus to analyse the structural stability and flexibility of BpAP under various conditions. Experiments verified this strategy is an effective way to improve the anti-autolytic ability of BpAP. Among the 28 mutants of BpAP, 5 mutants showed increases in thermal stability, pH stability, and storage stability in detergent, indicating a significant enhancement in their anti-autolytic capacity. Structural analysis and MD simulations confirmed that the enhanced stability characteristic of BpAP is attributed to improved anti-autolytic ability rather than increased structural stability. The three points combined mutant (MT5) showed the best increases in autolytic ability, as well as advanced catalytic efficiency. The low rate of inactive mutants and the high rate of positive mutants indicated that newly introduced screening factors (distance from catalytic residues, Gibbs free energy term, molecular simulation, and visual inspections) greatly enhance the design of anti-autolytic alkaline protease. Additionally, these findings enhance the industrial use of alkaline protease in detergents and similar applications.

Effect of non-additive mixing on entropic bonding strength and phase behavior of binary nanocrystal superlattices.

Non-additive mixing plays a key role in the properties of molecular fluids and solids. In this work, the potential for athermal order-disorder phase transitions is explored in non-additive binary colloidal nanoparticles that form substitutionally ordered compounds, namely, for equimolar mixtures of octahedra + spheres, which form a CsCl lattice compound, and cubes + spheres, which form a NaCl crystal. Monte Carlo simulations that target phase coexistence conditions were used to examine the effect on compound formation of varying degrees of negative non-additivity created by component size asymmetry and by size-tunable indentations in the polyhedra's facets, intended to allow the nestling of neighboring spheres. Our results indicate that the stabilization of the compound crystal requires a relatively large degree of negative non-additivity, which depends on particle geometry and the packing of the relevant phases. It is found that negative non-additivity can be achieved in mixtures of large spheres and small cubes having no indentations and lead to the athermal crystallization of the NaCl lattice. For similarly sized components, athermal congruent transitions are attainable and non-additivity can be generated through indentations, especially for the cubes + spheres system. Increasing indentation leads to lower phase coexistence free energy and pressure in the cubes + spheres system but has the opposite effect in the octahedra + spheres system. These results indicate a stronger stabilizing effect on the athermal compound phase by the cubes' indentations, where a deeper nestling of the spheres leads to a denser compound phase and a larger reduction in the associated pressure-volume free-energy term.

Computational insights into inhibiting EphA2: Integrating structure-based virtual screening, docking, and molecular dynamics simulations for small molecule discovery.

Elevated expression and dysfunction of ephrin type A receptor-2 (EphA2) have been implicated in the initiation and progression of cancer, metastasis, and unfavorable clinical outcomes. A promising strategy to counteract this dysregulation involves the development of small-molecule inhibitors that target EphA2. Our study focuses on this objective. To initiate Structure-Based Virtual Screening (SBVS), we leveraged an advanced online platform, the Mcule database, which houses an extensive collection of millions of chemical compounds. Using drug similarity filters, we efficiently identified ten thousand potential hits. By further refining the selection through toxicity profiling, we prudently narrowed down the candidates to a more manageable set of 100 molecules. Using the Mcule Single Click, DockThor, and SwissDock tools, we conducted multi-scoring docking assessments of thirty-seven compounds that satisfied the ADME standards. A comprehensive evaluation of Gibbs binding free energy terms, as derived from these docking tools, facilitated the identification of top-ranking docking hits. Remarkably, among the known inhibitors, dasatinib displayed the most robust binding to EphA2 with an average ΔG of -9.0 kcal/mol. Intriguingly, alternatives have emerged in recent years. Notably, small molecules such as Mcule-1579910267 (ΔG: -9.3 kcal/mol), Mcule-1893218381 (ΔG: -9.2 kcal/mol), Mcule-3981378344 (ΔG: -9.3 kcal/mol), and Mcule-8617639093 (ΔG: -9.1 kcal/mol) exhibited a notably strong binding affinity to EphA2, rivaling dasatinib. Subsequently, the four leading ligands along with dasatinib were selected for the MD simulations. Our rigorous analyses during the MD simulation phase encompassing RMSD, RMSF, SASA, ΔGsolv, and Rg underscored the favorable stability of Mcule-8617639093. This compelling evidence ultimately signifies the potential for selective EphA2 inhibition.

Adsorption characteristics of Janus tadpole polymers

The shape of Janus particles is directly connected to their adsorption behavior. Janus tadpole polymers offer a unique topological architecture that includes competition between entropic, enthalpic, and topological terms in the adsorption free energy; accordingly, non-trivial adsorption behavior patterns are expected. We study the surface adsorption of Janus tadpole polymers by means of Monte Carlo simulations, finding that, depending on which part of the tadpole polymers is preferentially adsorbing on the surface, very different types of behavior for both the adsorbed polymeric phase and of the brush arise. The adsorbed phase and the brush mutually influence each other, leading to a variety of phenomena such as nematic ordering of the adsorbed stiff tadpole tails and intriguing changes in the territoriality of adsorbed ring polymers on the surface. We analyze in detail our findings, revealing the mechanisms behind the organization and ordering, and opening up new possibilities to tune and control the structure of such systems.

Second inflection point of supercooled water surface tension induced by hydrogen bonds: A molecular-dynamics study.

Surface tension of supercooled water is a fundamental property in various scientific processes. In this study, we perform molecular dynamics simulations with the TIP4P-2005 model to investigate the surface tension of supercooled water down to 220K. Our results show a second inflection point (SIP) in the surface tension at temperature TSIP ≈ 267.5 ± 2.3K. Using an extended IAPWS-E functional fit for the water surface tension, we calculate the surface excess internal-energy and entropy terms of the excess Helmholtz free energy. Similar to prior studies [Wang et al., Phys. Chem. Chem. Phys. 21, 3360 (2019); Gorfer et al., J. Chem. Phys. 158, 054503 (2023)], our results show that the surface tension is governed by two driving forces: a surface excess entropy change above the SIP and a surface excess internal-energy change below it. We study hydrogen-bonding near the SIP because it is the main cause of water's anomalous properties. With decreasing temperature, our results show that the entropy contribution to the surface tension reaches a maximum slightly below the SIP and then decreases. This is because the number of hydrogen bonds increases more slowly below the SIP. Moreover, the strengths and lifetimes of the hydrogen bonds also rise dramatically below the SIP, causing the internal-energy term to dominate the excess surface free energy. Thus, the SIP in the surface tension of supercooled TIP4P-2005 water is associated with an increase in the strengths and lifetimes of hydrogen bonds, along with a decrease in the formation rate (#/K) of new hydrogen bonds.

S.O.S: Shape, orientation, and size tune solvation in electrocatalysis.

Current models to understand the reactivity of metal/aqueous interfaces in electrochemistry, e.g., volcano plots, are based on the adsorption free energies of reactants and products, which are often small hydrophobic molecules (such as in CO2 and N2 reduction). Calculations played a major role in the quantification and comprehension of these free energies in terms of the interactions that the reactive species form with the surface. However, solvation free energies also come into play in two ways: (i) by modulating the adsorption free energy together with solute-surface interactions, as the solute has to penetrate the water adlayer in contact with the surface and get partially desolvated (which costs free energy); (ii) by regulating transport across the interface, i.e., the free energy profile from the bulk to the interface, which is strongly non-monotonic due to the unique nature of metal/aqueous interfaces. Here, we use constant potential molecular dynamics to study the solvation contributions, and we uncover huge effects of the shape and orientation (on top of the already known size effect) of small hydrophobic and amphiphilic solutes on their adsorption free energy. We propose a minimal theoretical model, the S.O.S. model, that accounts for size, orientation, and shape effects. These novel aspects are rationalized by recasting the concepts at the base of the Lum-Chandler-Weeks theory of hydrophobic solvation (for small solutes in the so-called volume-dominated regime) into a layer-by-layer form, where the properties of each interfacial region close to the metal are explicitly taken into account.

SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes

Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets. In contrast to DFT, SQM2.20 provides affinity predictions in minutes, making it suitable for practical applications in hit identification or lead optimization.

Membrane Binding Strength vs Pore Formation Cost─What Drives the Membrane Permeation of Nanoparticles Coated with Cell-Penetrating Peptides?

Cell-penetrating peptides (CPPs) enable the transport of nanoparticles through cell membranes. Using molecular simulations, we conduct an in-depth investigation into the thermodynamic forces governing the passive translocation of CPP-coated nanoparticles across lipid bilayers, contrasting their behavior with that of bare particles to dissect the contribution of the peptides. Our analysis unveils a distinctive two-stage translocation mechanism, where the adsorption energy of the particles overcomes the cost of forming a hydrophilic transmembrane pore. Proper evaluation of the translocation mechanisms is only possible when using two reaction coordinates, in particular, one that explicitly includes the density of the lipids on the binding site of the particle. An analysis of adsorption and activation free energies in terms of a simple kinetic model provides a clearer understanding of the CPP effect. Experimental validation using nonendocytic cells confirms the superior membrane permeation of CPP-coated particles. Our findings have implications for the rational design of more efficient cell-permeating particles.

Enhanced mechanical interlocking of adhesive-bonded joints via tailored serrated patterns manufactured with laser ablation

ABSTRACT Laser ablation is currently used as an effective alternative to mechanical or chemical surface pre-treatments for adhesive-bonded joints due to benefits in terms of adherend surface morphology and surface free energy. Several works have seen production of micro-scale textures on both metallic and polymeric substrates via 3D printing, while others have sought to modify the macroscopic topography by generating serrated profiles on adherends prior to joint assembly. In this work, laser ablation has been used to create micro-scale tooth-like interlocking features forming structured patterns with complementary profiles on aluminium adherends of single lap joints. In a first set of experiments, laser processing parameters were varied while an optical profiler was used to quantify the geometry of induced ablation craters and lines while assessing the distribution of re-melt in and around the exposed region. Subsequently, an ablation strategy was developed to achieve specific interlocking features. Finally, different symmetrical and asymmetrical patterns were generated for each pair of coupled adherends while differentiating the orientation of features with respect to the load direction. The results confirm the critical role that laser ablation plays in strengthening adhesive bonded-joints, with interlocking features providing additional benefits depending on the structure type and load direction.

Polar Effects in Hydrogen Atom Transfer Reactions from a Proton-Coupled Electron Transfer (PCET) Perspective: Abstractions from Toluenes.

Rate constants for hydrogen atom transfer (HAT) reactions of substituted toluenes with tert-butyl, tert-butoxy, and tert-butylperoxyl radicals are reanalyzed here using the free energies of related proton transfer (PT) and electron transfer (ET) reactions, calculated from an extensive set of compiled or estimated pKa and E° values. The Eyring activation energies ΔGHAT‡ do not correlate with the relatively constant ΔG°HAT, but do correlate close-to-linearly with ΔG°PT and ΔG°ET. The slopes of correlations are similar for the three radicals except that the tBu• barriers shift in the opposite direction from the oxyl radical barriers─a clear example of the qualitative "polar effect" in HAT reactions. When cast quantitatively in free energy terms (ΔGHAT‡ vs ΔG°PT/ET), this effect is very small, only 5-10% of the typical Bell-Evans-Polanyi (BEP) effect of changing ΔG°HAT. This analysis also highlights connections between polar effects and the concepts of "asynchronous" or "imbalanced" HAT reactions in which the PT and ET components of ΔG°HAT contribute differently to the barrier. Finally, these observations are discussed in light of the traditional explanations of polar effects and the potential for a rubric that could predict the extent to which contra-thermodynamic selectivity may be achieved in HAT reactions.

A certain counterpart in dissipative setting of the Noether theorem with no dissipation pseudo-potentials.

We look at a mechanical dissipation inequality differing from the standard one by what we call a relative power, a notion that is appropriate in the presence of material mutations. We prove that a requirement of structural invariance for such an inequality under the action of diffeomorphism-based changes of observers (covariance) implies (i) the representation of contact actions in terms of the first Piola-Kirchhoff stress, (ii) local balances of standard and configurational actions, (iii) a priori constitutive restrictions in terms of free energy, and(iv) a representation of viscous-type stress components. This article is part of the theme issue 'Foundational issues, analysis and geometry in continuum mechanics'.

Effect of Scaling the Electrostatic Interactions on the Free Energy of Transfer of Azurin from Water to Lipid Membrane Determined by Coarse-Grained Simulations

Azurin protein potentially plays an important role as an anti-cancer therapeutic agent, particularly in treating breast cancer in experiments and showing without having a negative effect on normal cells. Although the interaction mechanism between protein and lipid membrane is complicated, it can be modeled as protein-lipid interaction. Since the all-atom (AA) model simulation is cost computing, we apply a coarse-grained (CG-MARTINI) model to calculate the protein-lipid interaction. We investigate the binding free energy value dependency by varying the windows separation and electrostatic scale parameters. After scaling the electrostatic interactions by a factor of 0.04, the best result in terms of free energy is -140.831 kcal/mol, while after window-separation optimization, it reaches -71.859 kcal/mol. This scaling was necessary because the structures from the CG MARTINI model have a higher density than the corresponding all-atom structures. We thus postulate that electrostatic interactions should be scaled down in this case of CG-MARTINI simulations.

Calculation of the Phase Diagrams (T – X and T – P) and the Thermodynamic Quantities for the Solid – Liquid Equilibria in n-tridecane

The solid – liquid equilibria in n-tridecane is investigated by calculating phase diagrams and the thermodynamic quantities using the Landau phenomenological model. By expanding the free energy in terms of the order parameter of the solid phase, the phase line equations are fitted to the experimental data for the T – X and T – P phase diagrams from the literature. The temperature dependences of the thermodynamic quantities (order parameter ψ, susceptibility χ_ψ, free energy F, the heat capacity C, entropy S and the enthalpy H) are predicted for the n-tridecane from this model. Our results give that the slope dT⁄dP≅2 "K/MPa" for n-C13 to n-C17. ψ varies with T as ψ~(T-T_m )^(1⁄2) above T_m. It is linear for the 〖χ_ψ〗^(-1), S(T) and C(T), and quadratic for the F(T) and H(T) in n-tridecane. This indicates that the Landau model, describes the observed behaviour of the phase diagrams satisfactorily for the solid – liquid equilibria in n-tridecane. Predictions of the thermodynamic quantities can also be compared with the measurements and predictions of some other theoretical models. The pressure effect, in particular, on the solid – liquid equilibria in n-tridecane can also be investigated under the model studied here.

Free-Base Corrole Anion.

Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been structurally characterized until now. Presented here is a first crystal structure of a free-base corrole anion, derived from tris(p-cyanophenyl)corrole, as the tetrabuylammonium salt. The low-temperature (100 K) structure reveals localized hydrogens on a pair of opposite pyrrole nitrogens. DFT calculations identify such a structure as the global minimum but also point to two cis tautomers only 4-7 kcal/mol above the ground state. In terms of free energy, however, the cis tautomers are above or essentially flush with the trans-to-cis barrier so the cis tautomers are unlikely to exist or be observed as true intermediates. Thus, the hydrogen bond within each dipyrrin unit on either side of the molecular pseudo-C2 axis through C10 (i.e., between pyrrole rings A and B or between C and D) qualifies as or closely approaches a low-barrier hydrogen bond. Proton migration across the pseudo-C2 axis entails much higher activation energies >20 kcal/mol, reflecting the relative rigidity of the molecule along the C1-C19 pyrrole-pyrrole linkage.

Acid Radical Tolerance of Silane Coatings on Calcium Silicate Hydrate Surfaces in Aggressive Environments: The Role of Nitrate/Sulfate Ratio.

Silane is known as an effective coating for enhancing the resistance of concrete to harmful acids and radicals that are usually produced by the metabolism of microorganisms. However, the mechanism of silane protection is still unclear due to its nanoscale attributes. Here, the protective behavior of silane on the calcium silicate hydrate (C-S-H) surface is examined under the attack environment of nitrate/sulfate ions using molecular dynamics simulations. The findings revealed that silane coating improved the resistance of C-S-H to nitrate/sulfate ions. This resistance is considered the origin of silane protection against harmful ion attacks. Further research on the details of molecular structures suggests that the interaction between the oxygen in the silane molecule and the calcium in C-S-H, which can prevent the coordination of sulfate and nitrate to calcium on the C-S-H surface, is the cause of the silane molecules' strong adsorption. These results are also proved in terms of free energy, which found that the adsorption free energy on the C-S-H surface followed the order silane > sulfate > nitrate. This research confirms the excellent protection performance of silane on the nanoscale. The revealed mechanism can be further used to help the development of high-performance composite coatings.

In Vitro Evaluation of Ag- and Sr-Doped Hydroxyapatite Coatings for Medical Applications.

Osseointegration plays the most important role in the success of an implant. One of the applications of hydroxyapatite (HAp) is as a coating for metallic implants due to its bioactive nature, which improves osteoconduction. The purpose of this research was to assess the in vitro behavior of HAp undoped and doped with Ag and/or Sr obtained by galvanostatic pulsed electrochemical deposition. The coatings were investigated in terms of chemical bonds, contact angle and surface free energy, electrochemical behavior, in vitro biomineralization in acellular media (SBF and PBS), and biocompatibility with preosteoblasts cells (MC3T3-E1 cell line). The obtained results highlighted the beneficial impact of Ag and/or Sr on the HAp. The FTIR spectra confirmed the presence of hydroxyapatite within all coatings, while in terms of wettability, the contact angle and surface free energy investigations showed that all surfaces were hydrophilic. The in vitro behavior of MC3T3-E1 indicated that the presence of Sr in the HAp coatings as a unique doping agent or in combination with Ag elicited improved cytocompatibility in terms of cell proliferation and osteogenic differentiation. Therefore, the composite HAp-based coatings showed promising potential for bone regeneration applications.

On the resurgent structure of quantum periods

Quantum periods appear in many contexts, from quantum mechanics to local mirror symmetry. They can be described in terms of topological string free energies and Wilson loops, in the so-called Nekrasov-Shatashvili limit. We consider the trans-series extension of the holomorphic anomaly equations satisfied by these quantities, and we obtain exact multi-instanton solutions for these trans-series. Building on this result, we propose a unified perspective on the resurgent structure of quantum periods. We show for example that the Delabaere-Pham formula, which was originally obtained in quantum mechanical examples, is a generic feature of quantum periods. We illustrate our general results with explicit calculations for the double-well in quantum mechanics, and for the quantum mirror curve of local \mathbb{P}^2ℙ2.

Thermodynamic Model of the Fluid System H2O–CO2–NaCl–CaCl2 at P-T Parameters of the Middle and Lower Crust

Based on the earlier obtained equations of state for the ternary systems H2O–CO2–CaCl2 and H2O–CO2–NaCl, an equation of state for the four-component fluid system H2O–CO2–NaCl–CaCl2 is derived in terms of the Gibbs excess free energy. A corresponding numerical thermodynamic model is built. The main part of the numerical parameters of the model coincides with the corresponding parameters of the ternary systems. The NaCl–CaCl2 interaction parameter was obtained from the experimental liquidus of the salt mixture. Similar to the thermodynamic models for H2O–CO2–CaCl2 and H2O–CO2–NaCl, the range of applicability of the model is pressure 1–20 kbar and temperature from 500 to 1400°C. The model makes it possible to predict the physicochemical properties of the fluid involved in most processes of deep petrogenesis: the phase state of the system (homogeneous or multiphase fluid, presence or absence of solid salts), chemical activities of the components, densities of the fluid phases, and concentrations of the components in the coexisting phases. The model was used for a detailed study of the phase state and activity of water on the H2O–CO2–salt sections when changing the ratio {{{{x}_{{{text{NaCl}}}}}} mathord{left/ {vphantom {{{{x}_{{{text{NaCl}}}}}} {({{x}_{{{text{NaCl}}}}} + {{x}_{{{text{CaC}}{{{text{l}}}_{{text{2}}}}}}})}}} right. kern-0em} {({{x}_{{{text{NaCl}}}}} + {{x}_{{{text{CaC}}{{{text{l}}}_{{text{2}}}}}}})}} from 1 to 0. Changes in the composition and density of coexisting fluid phases at a constant activity of water and changes in the total composition of the system are studied. A set of phase diagrams on sections H2O–NaCl–CaCl2 for different mole fractions of CO2 is obtained. Pressure dependencies of the maximal activity of water in the field of coexisting unmixable fluid phases are obtained for several salt compositions of the system. Due to removal of restrictions resulting from a smaller number of components in ternary systems, the thermodynamic behavior of systems with a mixed composition of the salt significantly differs from the behavior of those with a single salt component.

A novel continuum mechanical framework for decoupled material behavior in thickness and in-plane directions

A novel continuum mechanical framework for decoupling the material behavior in in-plane and thickness directions is presented that is motivated by the macroscopic behavior of paper and paperboard. Due to the manufacturing process of these composite materials and the underlying microstructure resulting thereof, the material response is highly anisotropic and can be divided into in-plane and out-of-plane behavior that is independent of each other. This decoupling is mostly incorporated in existing material models by setting the corresponding material parameters to zero which limits the models to an extension to nonlinear problems and is restrictive from a continuum mechanical point of view.Therefore, the aim of this paper is to derive a continuum mechanical framework that captures the in-plane and out-of-plane decoupling in a thermodynamically consistent manner for large deformations. Thus, the right Cauchy–Green deformation tensor was split into in-plane and out-of-plane deformations by use of structural tensors that were aligned with the preferential material directions. Therefore, the Helmholtz free energy was formulated in terms of modified invariants of the deformation tensor for in-plane and out-of-plane deformations separately, which lead to a decoupled framework that could easily be modified due to the flexible formulation of the Helmholtz free energy terms. The extension to inelasticity, in particular viscoelasticity here, was straightforward due to the split of the deformation tensor. Finally, the decoupling of the in-plane and out-of-plane response of the presented framework was demonstrated by structural examples for elastic and inelastic material behavior.The presented model incorporates the split into in-plane and out-of-plane behavior in a continuum mechanical manner, and thus, is a flexible constitutive framework for decoupled material responses that can easily be adjusted to different material behavior.

A Combination of Virtual and Experimental Screening Tools for the Prediction of Nitrofurantoin Multicomponent Crystals with Pyridine Derivatives

Thirty-four binary systems of nitrofurantoin with pyridine derivatives were analyzed by combining virtual (molecular complementarity prediction and hydrogen bond propensity calculations) and experimental (liquid-assisted grinding) screening methods. A new modification of the hydrogen bond propensity calculation method (the integrated hydrogen bond propensity calculation method) with significantly improved virtual screening efficiency was proposed. Novel cocrystals of nitrofurantoin with 3-aminopyridine and 2-(1H-Imidazol-2-yl)pyridine were discovered. The crystal structures of the new cocrystals were determined from single-crystal X-ray diffraction data, and the hydrogen bond patterns were studied in conjunction with the Molecular Electrostatic Potential maps of the components. The nitrofurantoin cocrystal with 3-aminopyridine was found to exist in two polymorphic modifications. The origins of the different stability of the polymorphic forms were rationalized both in terms of total lattice enthalpy and free energy derived from periodic DFT-D3 calculations and in terms of the non-covalent interaction energy distribution in crystal.