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Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.

We propose a three-dimensional model implementing a self-consistent field (SCF) mathematical formulation to predict the equilibrium orientation and morphology of grafted nanoparticles (NPs) in a polymer, based on two- and multibody interactions developed among them. First, we investigate the potential of mean force (PMF) between two spherical polystyrene-grafted silica NPs in a polystyrene melt as a function of the matrix-to-grafted chain length ratio and, more importantly, of the distribution of grafting points on their surfaces. While the most common assumption when performing such calculations is an equidistant distribution of grafting points on the surfaces of the NPs, we demonstrate here that the pattern of grafting plays an essential role in the equilibrium orientation and shape assumed by the particles inside the polymer matrix. In equidistant grafting, the role of grafting density is dominant, but, when grafting the chains irregularly, the same number of grafted chains distributed differently can significantly affect the self-assembly tendencies of the particles and the thermodynamic behavior of the composite system. Next, we calculate the free energy of a system of multiple equidistantly grafted nanoparticles exposed to a melt when they are arranged in a simple cubic (SC), body-centered cubic (BCC), and face-centered cubic (FCC) lattice as a function of their spatial density. We minimize the free energy with respect to nanoparticle density to impose the condition of thermodynamic equilibrium. Among the three arrangements, the FCC/SC is the most/least stable configuration. The three-dimensional SCF methodology proposed herein addresses all possible degrees of freedom for the molecular-level design of both stable dispersions and self-assembled nanocomposite morphologies with tailor-made properties. It offers a cost-effective approach to creating high-value nanocomposite materials such as polymer-matrix nanocomposites in the rubber industry as well as "particle-solids," the latter combining toughness with good optical properties. [ABSTRACT FROM AUTHOR]

The interaction between water and graphene is important for understanding the thermodynamic and kinetic properties of water on hydrophobic surfaces. In this study, we constructed a high-dimensional potential energy surface (PES) for the water-graphene system using the many-body expansion scheme and neural network fitting. By analyzing the landscape of the PES, we found that the water molecule exhibits a weak physisorption behavior with a binding energy of about − 1000 cm−1 and a very low diffusion barrier. Furthermore, extensive molecular dynamics were performed to investigate the adsorption and diffusion dynamics of a single water on a graphene surface at temperatures ranging from 50 to 300 K. Potential-of-mean-forces were computed from the trajectories, providing a comprehensive and accurate description of the water-graphene interaction kinetics.

Since solid-liquid interfacial nanobubbles (INBs) were first imaged, their long-term stability and large contact angle have been perplexing scientists. This study aimed to investigate the influence of internal gas density and external gas monolayers on the contact angle and stability of INB using molecular dynamics simulations. First, the contact angle of a water droplet was simulated at different nitrogen densities. The results showed that the contact angle increased sharply with an increase in nitrogen density, which was mainly caused by the decrease in solid-gas interfacial tension. However, when the nitrogen density reached 2.57 nm−3, an intervening gas monolayer (GML) was formed between the solid and water. After the formation of GML, the contact angle slightly increased with increasing gas density. The contact angle increased to 180° when the nitrogen density reached 11.38 nm−3, indicating that INBs transformed into a gas layer when they were too small. For substrates with different hydrophobicities, the contact angle after the formation of GML was always larger than 140° and it was weakly correlated with substrate hydrophobicity. The increase in contact angle with gas density represents the evolution of contact angle from macro- to nano-bubble, while the formation of GML may correspond to stable INBs. The potential of mean force curves demonstrated that the substrate with GML could attract gas molecules from a longer distance without the existence of a potential barrier compared with the bare substrate, indicating the potential of GML to act as a gas-collecting panel. Further research indicated that GML can function as a channel to transport gas molecules to INBs, which favors stability of INBs. This research may shed new light on the mechanisms underlying abnormal contact angle and long-term stability of INBs.

The emergence of multi-drug-resistant tuberculosis strains poses a significant challenge to modern medicine. The development of new antituberculosis drugs is hindered by the low permeability of many active compounds through the extremely strong bacterial cell wall of mycobacteria. In order to estimate the ability of potential antimycobacterial agents to diffuse through the outer mycolate membrane, the free energy profiles, the corresponding activation barriers, and possible permeability modes of passive transport for a series of known antibiotics, modern antituberculosis drugs, and prospective active drug-like molecules were determined using molecular dynamics simulations with the all-atom force field and potential of mean-force calculations. The membranes of different chemical and conformational compositions, density, thickness, and ionization states were examined. The typical activation barriers for the low-mass molecules penetrating through the most realistic membrane model were 6–13 kcal/mol for isoniazid, pyrazinamide, and etambutol, and 19 and 25 kcal/mol for bedaquilin and rifampicin. The barriers for the ionized molecules are usually in the range of 37–63 kcal/mol. The linear regression models were derived from the obtained data, allowing one to estimate the permeability barriers from simple physicochemical parameters of the diffusing molecules, notably lipophilicity and molecular polarizability. [ABSTRACT FROM AUTHOR]

We study the interaction between a flat surface and a contaminant solution. The surface is protected by a grafted polymer layer. Our primary interest is to better understand and elucidate the effect of simple molecular interactions on the contamination and decontamination of the surface through molecular diffusion. These interactions manifest themselves in the potential of mean force that the contaminant molecule experiences as it diffuses across the grafted polymer layer. For simplicity, we consider that all interactions are of the hard-sphere type. The size of the contaminant molecule is the same as that of the solvent as well as the individual polymer segment. Despite these simplifications, the analysis offers important physical insights and a qualitative description of the contamination and decontamination processes. [ABSTRACT FROM AUTHOR]

Gas molecules or weakly interacting molecules are commonly observed to diffuse through and fill space. Therefore, when the molecules initially confined in one compartment are allowed to move through a channel into another empty compartment, we expect that some molecules will be transported into the initially empty compartment. In this work, we thermodynamically analyze this transport process using a simple model consisting of graphene plates, a carbon nanotube (CNT), and nonpolar molecules that are weakly interacting with each other. Specifically, we calculate the free energy change, or the potential of mean force (PMF), as the molecules are transported from one compartment to another compartment. The PMF profile clearly exhibits a global minimum, or a free energy well, at the state wherein the molecules are evenly distributed over the two compartments. To better understand the thermodynamic origin of the well, we calculate the energetic and entropic contributions to the formation of the well, and we show that the entropic change is responsible for it and is the driving force for transport. Our work not only enables a fundamental understanding of the thermodynamic nature of the transport of weakly interacting molecules with molecular details, but also provides a method for calculating the free energy change during transport between two separate spaces connected by a nanochannel. [ABSTRACT FROM AUTHOR]

The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure. [ABSTRACT FROM AUTHOR]

The voltage-gated proton channel Hv1 mediates efflux of protons from the cell. Hv1 integrally contributes to various physiological processes including pH homeostasis and the respiratory burst of phagocytes. Inhibition of Hv1 may provide therapeutic avenues for the treatment of inflammatory diseases, breast cancer, and ischemic brain damage. In this work, we investigate two prototypical Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI), and 5-chloro-2-guanidinobenzimidazole (GBIC), from an experimentally screened class of guanidine derivatives. Both compounds block proton conduction by binding the same site located on the intracellular side of the channel. However, when added to the extracellular medium, the compounds strongly differ in their ability to inhibit proton conduction, suggesting substantial differences in membrane permeability. Here, we compute the potential of mean force for each compound to permeate through the membrane using atomistic molecular dynamics simulations with the adaptive biasing force method. Our results rationalize the putative distinction between these two blockers with respect to their abilities to permeate the cellular membrane.

Food processing and consumption involves multiple contacts between biological fluids and solid materials of processing devices, of which steel is one of the most common. Due to the complexity of these interactions, it is difficult to identify the main control factors in the formation of undesirable deposits on the device surfaces that may affect safety and efficiency of the processes. Mechanistic understanding of biomolecule–metal interactions involving food proteins could improve management of these pertinent industrial processes and consumer safety in the food industry and beyond. In this work, we perform a multiscale study of the formation of protein corona on iron surfaces and nanoparticles in contact with cow milk proteins. By calculating the binding energies of proteins with the substrate, we quantify the adsorption strength and rank proteins by the adsorption affinity. We use a multiscale method involving all-atom and coarse-grained simulations based on generated ab initio three-dimensional structures of milk proteins for this purpose. Finally, using the adsorption energy results, we predict the composition of protein corona on iron curved and flat surfaces via a competitive adsorption model. [ABSTRACT FROM AUTHOR]

Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption. [ABSTRACT FROM AUTHOR]

Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area. [ABSTRACT FROM AUTHOR]

It is of great significance to explore the osmotic transport mechanisms across nanopores for the design and applications of forward osmosis membranes. To deeply understand the quantitative relationship between pore diameters and water transport across nanopores of forward osmosis membrane at molecular level, systematic molecular dynamic simulations are conducted on water transport behaviors across nanopores with a length of 16 Å and with diameters ranging from 8.14 to 16.28 Å. The phase interface barrier on water flux across nanopores is predicted by the potential of mean force and hydrogen-bonding number. The combined effects of water structure, interface barrier and flow resistance of nanopores, and hydrogen bonds on the water flux are analyzed. A non-monotonic profile of the water flux with respect to pore diameters is observed due to the fact that the water flux of forward osmosis is determined by the interface barrier and flow resistance being the same order of magnitude with the naturally osmotic pressure rather than the driven pressure which is one order of magnitude higher than the naturally osmotic pressure. For the pore diameters between 8.14 and 10.85 Å where water structures are highly ordered, the water flux increases with the increasing diameter owing to the combined effects of the increasing diffusion coefficients and decreasing potential of mean force and hydrogen-bonding number. The increasing low resistance within nanopores caused by the water structure transition to be disordered at a critical diameter of 12.21 Å takes account for the obviously decreasing water flux. For the pore diameter being greater than12.21 Å, a linear increase of the water flux with increasing diameter is ascribed to the stabilized diffusion coefficient, potential of mean force, and hydrogen-bonding number. [ABSTRACT FROM AUTHOR]

Glioblastoma (GBM) is a highly malignant primary brain tumor, and epidermal growth factor receptor (EGFR) is a well characterized biomaker on GBM. Treatment of GBM with EGFR inhibitors achieved limited efficacy due to low blood–brain barrier (BBB) permeability, and BBB-penetrant drugs are required. In this study, the BBB penetration of erlotinib and JN037 were studied using molecular dynamics method with explicit membrane model. The free energy profiles indicate that JCN037 has a lower central energy barrier than erlotinib, and it has a local minimum at lipid-water interface while erlotinib has not. Unconstrained MD simulations found that erlotinib prefers staying in water while JCN037 tends to interact with lipid molecules. Further analysis reveals that the Br atom of JCN037 plays an important role in its interaction with lipid molecules, and the adjacent F atom enhances the interaction of Br. The two flexible methoxyethoxy chains of erlotinib are responsible for its poor penetration. Our computational results agree well with the experimental results, providing useful information in the design and improvement of drugs with good BBB permeation. [ABSTRACT FROM AUTHOR]

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only a few simulation works have addressed the matter, which hampers a solid rationalization of the richness of outcomes observed in experiments. Particularly, to date, there are no theoretical works addressing the impact of hydropathy on the transport of a molecule within lipid mesophases, despite the significant fraction of hydrophobic molecules among currently-available drugs. Similarly, the high heterogeneity of water mobility in the nanoscopic channels within lipid mesophases has also been neglected. To fill this gap, we introduce here a minimal model to account for these features in a lamellar geometry, and systematically study the role played by hydropathy and water–mobility heterogeneity by Brownian-dynamics simulations. We unveil a fine interplay between the presence of free-energy barriers, the affinity of the drug for the lipids, and the reduced mobility of water in determining the net molecular transport. More in general, our work is an instance of how multiscale simulations can be fruitfully employed to assist experiments in release systems based on lipid mesophases. [ABSTRACT FROM AUTHOR]

• The influence of surface hydrophobicity on the potential of mean force between gas molecules and substrates was analyzed. • The correlation between the disruption of the hydration layer and the accumulation of gas molecules at the hydrophobic surface was revealed. • The temporal evolution of interfacial concentration of liquid and gas influenced by surface hydrophobicity and gas oversaturation were studied. • The influence of gas oversaturation level and surface hydrophobicity on INB nucleation time was investigated. Over the past two decades, extensive research efforts have been devoted to exploring the existence, stability, and applications of interfacial nanobubbles (INBs). However, investigations into the microscopic nucleation process of INBs have been relatively limited. In this study, we utilized molecular dynamics simulations to elucidate the nucleation dynamics of INBs , with a particular focus on examining the influence of surface hydrophobicity and gas oversaturation. Our findings revealed a distinct preference for INBs to form on hydrophobic surfaces compared to hydrophilic ones, which agrees well with the experimental results. Temporal evolution analysis of the interfacial density of gas and liquid near the solid–liquid interface indicated a gradual enrichment of gas molecules at the hydrophobic surface, accompanied by a gradual disruption of the hydration layer, phenomena not observed on hydrophilic surfaces. The affinity of gas molecules towards the hydrophobic surface was further confirmed by potential of mean force (PMF) analysis, which demonstrated a decrease in the energy barrier and an increase in the potential well with increasing surface hydrophobicity. Moreover, increasing bulk gas supersaturation and surface hydrophobicity both contribute to shortening the INB nucleation time, primarily due to the enhanced gas enrichment rate. Further studies indicated that the gas enrichment rate had a directly proportional linear relationship with the bulk gas concentration. However, as the surface hydrophobicity increased, the gas enrichment rate initially rose rapidly and then entered a plateau phase. This may be because, when surface hydrophobicity is strong, the gas enrichment rate becomes limited by the diffusion of gas molecules in the liquid. These findings offer valuable insights into the nucleation mechanism of INBs on hydrophobic surfaces under gas oversaturation, contributing to a deeper understanding of their behavior and potential applications. [ABSTRACT FROM AUTHOR]

We study the interaction between a flat surface and a contaminant solution. The surface is protected by a grafted polymer layer. Our primary interest is to better understand and elucidate the effect of simple molecular interactions on the contamination and decontamination of the surface through molecular diffusion. These interactions manifest themselves in the potential of mean force that the contaminant molecule experiences as it diffuses across the grafted polymer layer. For simplicity, we consider that all interactions are of the hard-sphere type. The size of the contaminant molecule is the same as that of the solvent as well as the individual polymer segment. Despite these simplifications, the analysis offers important physical insights and a qualitative description of the contamination and decontamination processes.

Gas molecules or weakly interacting molecules are commonly observed to diffuse through and fill space. Therefore, when the molecules initially confined in one compartment are allowed to move through a channel into another empty compartment, we expect that some molecules will be transported into the initially empty compartment. In this work, we thermodynamically analyze this transport process using a simple model consisting of graphene plates, a carbon nanotube (CNT), and nonpolar molecules that are weakly interacting with each other. Specifically, we calculate the free energy change, or the potential of mean force (PMF), as the molecules are transported from one compartment to another compartment. The PMF profile clearly exhibits a global minimum, or a free energy well, at the state wherein the molecules are evenly distributed over the two compartments. To better understand the thermodynamic origin of the well, we calculate the energetic and entropic contributions to the formation of the well, and we show that the entropic change is responsible for it and is the driving force for transport. Our work not only enables a fundamental understanding of the thermodynamic nature of the transport of weakly interacting molecules with molecular details, but also provides a method for calculating the free energy change during transport between two separate spaces connected by a nanochannel.

With the increasing complication of production and geology conditions, and the increase of mining intensity and depth in coal mine, the coal structure presents varying degrees of deformation. In order to study the influence of uniaxial tension–compression effect on mechanical properties of coal matrix and CH4/CO2 adsorption characteristics, a macromolecular model reflecting the realistic bituminous coal structure was established. Results demonstrate that the influence of tension strain on the microporous structural parameters is greater than that of compression strain, and the tension strain weakens the mechanical properties but enhances the adsorbates adsorption amount. For the pure gases adsorption, there is a negative linear correlation between the total energy and adsorption amount. Additionally, the strain ranging from −0.20 to 0.20, the distribution of punctated adsorbates density develops to that of banded adsorbates density, and the mean adsorption density and saturated adsorption amount increase linearly. For the binary components adsorption (1:1), the CH4 adsorption strength increases while the CO2 adsorption strength slightly decreases. The minimum of total energy decreases in a quadratic polynomial relationship with the strain, and the proportion of van der Waals energy is 75.8–85.5%. Nevertheless, the competitive adsorption and strain have little effect on the potential energy range of the adsorbates. Furthermore, the diffusibility of CO2 molecular layers is relatively good, and the strain enhances the stability of CH4 molecular layers for the saturated binary adsorption. The findings provide essential guidance for the improvement of carbon capture and storage and CO2-enhanced coalbed methane technologies in the deformation area of coal seam. [ABSTRACT FROM AUTHOR]

AZD3759 is an epidermal growth factor receptor inhibitor with good blood–brain barrier permeability, demonstrating encouraging activity against central nervous system metastases. However, the underlying mechanism was still unclear. In this study, the interaction between AZD3759 and membrane was studied with 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer as a model lipid. Both the cationic and neutral state of AZD3759 were considered in the simulations, and the results show that cationic AZD3759 forms more hydrogen bonds with bilayer than neutral AZD3759, and Coulombic interaction has great effects in the transmembrane process of cationic AZD3759. AZD3759 prefers to reside in the interface between the hydrophilic headgroup region and hydrophobic region of bilayer, and the chloroflurobenzene moiety plays a crucial role in the insertion of AZD3759. PMF results suggest that the hydrophobic region of DMPC bilayer is permeable by AZD3759. Understanding the transmembrane mechanism of AZD3759 at molecular level may provide useful information to the design and optimization of anti-tumor drugs with improved BBB penetration. • The penetration mechanism of AZD3759 with DMPC bilayer was studied by molecular dynamics simulations. • Neutral AZD3759 could penetrate deeper into DMPC bilayer than protonated AZD3759. • The chloroflurobenzene moiety plays a significant role in the insertion of AZD3759 into DMPC bilayer. • The electrostatic interaction is the driving force for the initial binding of AZD3759 to DMPC bilayer. • Our findings may enhance the mechanism understanding of drugs with good BBB permeability. [ABSTRACT FROM AUTHOR]

Water permeation through phospholipid/cholesterol bilayers is the key to understanding tension-induced rupture of biological cell membranes. We performed molecular dynamics simulations of stretched phospholipid/cholesterol bilayers to investigate changes in the free energy profile of water molecules across the bilayer and the lipid structure responsible for water permeation. We modeled stretching of the bilayer by applying areal strain. In stretched phospholipid/cholesterol bilayers, the hydrophobic tail of the phospholipids became disordered and the free energy barrier to water permeation decreased. Upon exceeding the critical areal strain, a phase transition to an interdigitated gel phase occurred before rupture, and the hydrophobic tail ordering as well as the free energy barrier were restored. In pure phospholipid bilayers, we did not observe such recoveries. These transient recoveries in the phospholipid/cholesterol bilayer suppressed water permeation and membrane rupture, followed by an increase in the critical areal strain at which the bilayer ruptured. This result agrees with experimental results and provides a reasonable molecular mechanism for the toughness of phospholipid/cholesterol bilayers under tension.Communicated by Ramaswamy H. Sarma.

Food processing and consumption involves multiple contacts between biological fluids and solid materials of processing devices, of which steel is one of the most common. Due to the complexity of these interactions, it is difficult to identify the main control factors in the formation of undesirable deposits on the device surfaces that may affect safety and efficiency of the processes. Mechanistic understanding of biomolecule–metal interactions involving food proteins could improve management of these pertinent industrial processes and consumer safety in the food industry and beyond. In this work, we perform a multiscale study of the formation of protein corona on iron surfaces and nanoparticles in contact with cow milk proteins. By calculating the binding energies of proteins with the substrate, we quantify the adsorption strength and rank proteins by the adsorption affinity. We use a multiscale method involving all-atom and coarse-grained simulations based on generated ab initio three-dimensional structures of milk proteins for this purpose. Finally, using the adsorption energy results, we predict the composition of protein corona on iron curved and flat surfaces via a competitive adsorption model.

In this study, we investigated thermodynamic inconsistency in the potential of mean force (PMF) calculated using the Ornstein-Zernike (OZ), one-dimensional reference interaction site model (1D-RISM), and three-dimensional OZ (3D-OZ) theories. Two methods were used to obtain the PMF: converting the radial distribution function (RDF) into the PMF, and utilizing the solvation free energy (SFE) of the diatomic solute molecule with an added direct interaction between the two solute atoms. Both for the Lennard-Jones (LJ) and Coulomb systems, the hypernetted chain (HNC) closure showed the best performance among the closure relationships tested in this study. However, the performance of the HNC was not perfect and exhibited significant inconsistency in the PMF. The Kovalenko–Hirata and Kobryn–Gusarov–Kovalenko closures were also tested, with fair results when combined with the 1D-RISM equation but poor results when combined with the 3D-OZ equation. The Verlet-modified (VM) closure was found to be inapplicable to Coulomb systems. In contrast, the modified HNC (MHNC) closure showed relatively good results at high temperatures. Furthermore, we modified the Martynov–Sarkisov (MS) closure for Coulomb systems, resulting in a modified MS closure that yields relatively accurate PMF results. We also discuss the behavior of the SFE for Coulomb systems obtained from the 1D-RISM theory, a thorough analysis of both the RDF and the integrand in the Kirkwood charging formula. [ABSTRACT FROM AUTHOR]

Sugammadex, marketed as Bridion™, is an approved cyclodextrin (CD) based drug for the reversal of neuromuscular blockade in adults undergoing surgery. Sugammadex forms an inclusion complex with the neuromuscular blocking agent (NMBA) rocuronium, allowing rapid reversal of muscle paralysis. In silico methods have been developed for studying CD inclusion complexes, aimed at accurately predicting their structural, energetic, dynamic, and kinetic properties, as well as binding constants. Here, a computational study aimed at characterizing the sugammadex-rocuronium system from the perspective of docking calculations, free molecular dynamics (MD) simulations, and biased metadynamics simulations with potential of mean force (PMF) calculations is presented. The aim is to provide detailed information about this system, as well as to use it as a model system for validation of the methods. This method predicts results in line with experimental evidence for both the optimal structure and the quantitative value for the binding constant. Interestingly, there is a less profound preference for the orientation than might be assumed based on electrostatic interactions, suggesting that both orientations may exist in solution. These results show that this technology can efficiently analyze CD inclusion complexes and could be used to facilitate the development and optimization of novel applications for CDs. [Display omitted] [ABSTRACT FROM AUTHOR]

Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area.

The interaction of antimicrobial and amyloid peptides with cell membranes is a critical step in their activities. Peptides of the uperin family obtained from the skin secretion of Australian amphibians demonstrate antimicrobial and amyloidogenic properties. All-atomic molecular dynamics and an umbrella sampling approach were used to study the interaction of uperins with model bacterial membrane. Two stable configurations of peptides were found. In the bound state, the peptides in helical form were located right under the head group region in parallel orientation with respect to the bilayer surface. Stable transmembrane configuration was observed for wild-type uperin and its alanine mutant in both alpha-helical and extended unstructured forms. The potential of mean force characterized the process of peptide binding from water to the lipid bilayer and its insertion into the membrane, and revealed that the transition of uperins from the bound state to the transmembrane position was accompanied by the rotation of peptides and passes through the energy barrier of 4–5 kcal/mol. Uperins have a weak effect on membrane properties.

To investigate the amphiphilicity of cellulose, a series of molecular dynamics simulations were performed with a cellulose nanocrystal and a water–octane interfacial system. Assuming that the axis of cellulose is parallel to the water–octane interface, the freedoms of motion of the nanocrystal were restricted to two, the distance from the interface and the orientation around the axis. The mean force and the mean torque on the nanocrystal were evaluated with sufficiently long simulation at each crystal configuration, and their numerical integration gave a smooth free energy surface as the potential of mean force. The cellulose sample used here was found to be much more hydrophilic than oleophilic with the free energy difference Δ F w → o = 318 kcal/mol. Three adsorption states with local minimum of adsorption free energy are distinguished in the free energy surface—the direct contact type which is similar to previously reported one, the hydrophilic-surface/water/octane type where a thin water layer is sandwiched between the surface and the octane phase, and the oleophilic/water/octane type where a thin water layer also exists. Water molecules in these water layers contribute to stabilize the adsorption states by taking a special orientational order and slow self-diffusion. [ABSTRACT FROM AUTHOR]

We report the results of our participation in the SAMPL8 GDCC Blind Challenge for host-guest binding affinity predictions. Absolute binding affinity prediction is of central importance to the biophysics of molecular association and pharmaceutical discovery. The blinded SAMPL series have provided an important forum for assessing the reliability of binding free energy methods in an objective way. In this challenge, we employed two binding free energy methods, the newly developed alchemical transfer method (ATM) and the well-established potential of mean force (PMF) physical pathway method, using the same setup and force field model. The calculated binding free energies from the two methods are in excellent quantitative agreement. Importantly, the results from the two methods were also found to agree well with the experimental binding affinities released subsequently, with R values of 0.89 (ATM) and 0.83 (PMF). These results were ranked among the best of the SAMPL8 GDCC challenge and second only to those obtained with the more accurate AMOEBA force field. Interestingly, the two host molecules included in the challenge (TEMOA and TEETOA) displayed distinct binding mechanisms, with TEMOA undergoing a dehydration transition whereas guest binding to TEETOA resulted in the opening of the binding cavity that remains essentially dry during the process. The coupled reorganization and hydration equilibria observed in these systems is a useful prototype for the study of these phenomena often observed in the formation of protein-ligand complexes. Given that the two free energy methods employed here are based on entirely different thermodynamic pathways, the close agreement between the two and their general agreement with the experimental binding free energies are a testament to the high quality and precision achieved by theory and methods. The study provides further validation of the novel ATM binding free energy estimation protocol and paves the way to further extensions of the method to more complex systems. [ABSTRACT FROM AUTHOR]

The dynamic, structure, and thermodynamic properties of sulfur dioxide guest gas inside nanoporous fixed silica Y zeolite were studied by molecular dynamics simulation at different loadings of SO2 per unit cell and within a range of temperature. At loading 20, greater deviation from Fickian behavior is observed. Generally, self-diffusion coefficient increases with temperature. The activation energy for diffusion follows a decreasing trend by loading increase, except at loading 20, which shows an increase in activation energy. The velocity autocorrelation function demonstrates oscillating behavior and cage effect decrease with temperature. From the radial distribution function (RDF) between gas and zeolite framework, it is found that the first layer around the central atom at a low temperature is established more easily and the first peak of the RDF appears at a short distance with more intensity. The interaction between S and Si atoms was examined by the potential of mean force that is independent of loading. The results indicate that SO2 is able to disperse homogeneously into the zeolite at all concentrations and temperatures without much perturbation.

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only a few simulation works have addressed the matter, which hampers a solid rationalization of the richness of outcomes observed in experiments. Particularly, to date, there are no theoretical works addressing the impact of hydropathy on the transport of a molecule within lipid mesophases, despite the significant fraction of hydrophobic molecules among currently-available drugs. Similarly, the high heterogeneity of water mobility in the nanoscopic channels within lipid mesophases has also been neglected. To fill this gap, we introduce here a minimal model to account for these features in a lamellar geometry, and systematically study the role played by hydropathy and water–mobility heterogeneity by Brownian-dynamics simulations. We unveil a fine interplay between the presence of free-energy barriers, the affinity of the drug for the lipids, and the reduced mobility of water in determining the net molecular transport. More in general, our work is an instance of how multiscale simulations can be fruitfully employed to assist experiments in release systems based on lipid mesophases.

Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.

Due to their physical properties including high thermal stability, very low vapor pressure, and high microwave absorption, ionic liquids have attracted great attention as solvents for the synthesis of nanomaterials, being considered as greener alternatives to traditional solvents. While usual solvents often need additives like surfactants, polymers, or other ligands to avoid nanoparticle coalescence, some ionic liquids can stabilize nanoparticles in dispersion without any additive. In order to quantify how the ionic liquids can affect both the aggregation thermodynamics and kinetics, molecular dynamics simulations were performed to simulate the evolution of concentrated dispersions and to compute the potential of mean force between nanoparticles of both hydrophilic and hydrophobic natures in two imidazolium-based ionic liquids, which differ from each other by the length of the cation alkyl group. Depending on the nature of the nanoparticle, structured layers of the polar and apolar regions of the ionic liquid can be formed close to its surface, and those layers lead to activation barriers for dispersed particles to get in contact. If the alkyl group of the ionic liquid is long enough to lead to domain segregation between the ionic and apolar portions of the solvent, the layered structure around the particle becomes more structured and propagates several nanometers away from its surface. This leads to stronger barriers close to the contact and also multiple barriers at larger distances that result from the unfavorable superposition of solvent layers of opposing nature when the nanoparticles approach each other. Those long-range solvent-mediated forces not only provide kinetic stability to dispersions but also affect their dynamics and lead to a long-range ordering between dispersed particles that can be explored as a template for the synthesis of complex materials.

Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis. [ABSTRACT FROM AUTHOR]

Sodium channels selectively conduct Na+ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na+ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na+ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations, we investigate the interaction of α-tocopherol (α-toc) with dipalmitoylphosphatidylcholine (DPPC), dimyristoylphosphatidylcholine (DMPC), palmitoyloleoylphosphatidylcholine (POPC), and palmitoyloleoylphosphatidylethanolamine (POPE) lipid bilayers. The goal is to develop a better understanding of the positioning and orientation of α-toc inside the bilayers; properties of significant relevance to α-toc anti-oxidant activity. We investigated bilayer systems with 128 lipids in the presence of either single or 14 α-toc molecules. The single α-toc bilayer systems were investigated via biased MD simulations in which the potential of mean force (PMF) and diffusivity were obtained as functions of the distance between α-toc head group and bilayer center. The higher α-toc concentration systems were investigated with unbiased MD simulations. For all four bilayers at both concentrations, the simulations show that the most probable location of the α-toc hydroxyl group is just below the lipid carbonyl group. Overall, the simulation results are in good agreement with existing experimental data except for the DMPC bilayer system for which some experiments predict α-toc to be located closer to bilayer center. The flip-flop frequency calculated shows that the α-toc flip-flop rate is sensitive to bilayer lipid type. In particular, α-toc has a much lower flip-flop rate in a POPE bilayer compared to the three PC lipid bilayers due to the smaller area per lipid in the POPE bilayer. For DMPC and POPC, the α-toc flip-flop rates are significantly higher at higher α-toc concentration and this appears to be related to the local structural disruption caused by α-toc clusters spanning the bilayer. [ABSTRACT FROM AUTHOR]

Salt ions play critical roles in the assembly of polyelectrolytes such as nucleic acids and colloids since ions can regulate the effective interactions between them. In this work, we investigated the effective interactions between oppositely charged particles in symmetrical (z:z) salt solutions by Monte Carlo simulations with salt valence z ranging from 1 to 4. We found that the effective interactions between oppositely charged particles are attractive for 1:1 and low multivalent salts, while they become apparently repulsive for high multivalent salts. Moreover, such effective repulsion becomes stronger as z increases from 2 to 3, while it becomes weaker when z increases from 3 to 4. Our analyses reveal that the overall effective interactions are attributed to the interplay between ion translational entropy and electrostatic energy, and the non-monotonic salt-valence dependence of the effective repulsions is caused by the rapid decrease of attractive electrostatic energy between two oppositely charged particles with their over-condensed counterions of opposite charges when z exceeds 3. Our further MC simulations show that the involvement of local-ranged counterion–co-ion repulsions can enhance the effective repulsions through weakening the attractive electrostatic energy, especially for higher salt valence.

We applied a new large two membrane model of human urea transporter B (UT-B) with urea concentration gradient between intracellular and extracellular solution to explore the structure and dynamics of urea permeation. The first solved human UT-B X-ray crystal structure (PDB 6QD5) was studied using atomistic force field based large scale molecular dynamics (MD) simulations. The urea binding sites in UT-B were identified by the combination of first principles molecular dynamics docking and hybrid steered molecular dynamics (hSMD). In the simulations, urea molecules bound to the two binding sites although urea molecules did not go through the channels. The potential of mean force (PMF) of urea along the channel was calculated by hSMD to investigate the selectivity of the urea permeation across the channel pore. The simulations provide an opportunity to explore the binding sites spontaneously to help understand the urea permeation gating and transportation mechanism. A clearer analysis of the selectivity filter is shown in more detail. We also furthered the research about small organic molecules in the specific environment, such as channels in this work. [ABSTRACT FROM AUTHOR]

The organization of genomes in space and time dimension plays an important role in gene expression and regulation. Chromatin folding occurs in a dynamic, structured way that is subject to biophysical rules and biological processes. Nucleosomes are the basic unit of chromatin in living cells, and here we report on the effective interactions between two nucleosomes in physiological conditions using explicit-solvent all-atom simulations. Free energy landscapes derived from umbrella sampling simulations agree well with recent experimental and simulation results. Our simulations reveal the atomistic details of the interactions between nucleosomes in solution and can be used for constructing the coarse-grained model for chromatin in a bottom-up manner.

Interfacial tensions play an important role in dewatering of hydrophilic materials like nanofibrillated cellulose, and are affected by the molecular organization of water at the interface. Application of an electric field influences the orientation of water molecules along the field direction. Hence, it should be possible to alter the interfacial free energies to tune the wettability of cellulose surface through application of an external electric field thus, aiding the dewatering process. Molecular dynamics simulations of cellulose surface in contact with water under the influence of an external electric field have been conducted with GLYCAM-06 forcefield. The effect of variation in electric field intensity and directions on the spreading coefficient has been addressed via orientational preference of water molecules and interfacial free energy analyses. The application of electric field influences the interfacial free energy difference at the cellulose-water interface. The spreading coefficient increases with the electric field directed parallel to the cellulose-water interface while it decreases in the perpendicular electric field. Variation in interfacial free energies seems to explain the change in contact angle adequately in presence of an electric field. The wettability of cellulose surface can be tuned by the application of an external electric field. [ABSTRACT FROM AUTHOR]

Cholesterol plays a crucial role in modulating the physicochemical properties of membranes, thus influencing the membrane transport of drugs. In this paper, the effects caused by cholesterol on the membrane transport of chlorzoxazone (CZX), a centrally acting muscle relaxant drug, were probed through molecular dynamics simulations. POPC was selected as the model lipid, and three different cholesterol concentrations (0%, 20%, and 50% CHOL) were considered. The outcomes reveal that the area per lipid of POPC decreases and the order parameter increases with enhanced concentration of CHOL. CZX prefers to localize at the interface between the headgroup region and the hydrophobic tail region of POPC, and the main energy barrier occurs in the hydrophobic region. The impact of CHOL on the free energy profile is correlated with concentration: low concentration facilitates CZX permeation, while high concentration hinders CZX permeation. Our findings coincide with experimental results, enhancing the mechanism understanding of how drug molecules are transported through membranes in the presence of CHOL. [ABSTRACT FROM AUTHOR]