Free energy calculations for molecular solids using GROMACS

In silico approaches for developing sesquiterpene derivatives as antagonists of human nicotinic acetylcholine receptors (nAChRs) for nicotine addiction treatment

Cinnamomum, a genus within the Lauraceae family, has gained global recognition due to its wide-ranging utility. Extensive research has been dedicated to exploring its phytochemical composition and pharmacological effects. Notably, the uniqueness of Cinnamomum lies in its terpenoid content, characterized by distinctive structures and significant biological implications. An intriguing discovery is that sesquiterpene compounds originating from Cinnamomum possess the capacity to function as antagonists for human nicotinic acetylcholine receptors (nAChRs), specifically the nAChRÿ3 subtype, rendering them potential candidates for nicotine replacement therapy (NRT) to aid active smokers. This investigation employed molecular docking and molecular dynamics simulations to assess the inhibitory effects of these compounds on nAChRÿ3. Among the 55 compounds examined, Dihydroxyeudesmene, Gibberodione, and Germacrene-E exhibited the highest binding affinities. These compounds demonstrated robust interactions with the nAChRÿ3 receptor, as evidenced by elevated molecular mechanics general surface area (MM/GBSA) values (ΔG Bind = Dihydroxyeudesmene: -36.45 kcal/mol, Gibberodione: -36.51 kcal/mol, and Germacrene-E: -36.51 kcal/mol). Molecular dynamics simulations further confirmed the stability of these three compounds, indicating their potential to effectively compete with native ligands. However, comprehensive in vitro, in vivo, and clinical investigations are imperative to ascertain the efficacy of these promising therapeutic candidates.

TIP 4 P 2005 Ice : Simulating water with two molecular states

Rigid, non-polarizable water models are very efficient from a computational point of view, and some of them have a great ability in predicting experimental properties. There is, however, little room for improvement in simulating water with this strategy, whose main shortcoming is that water molecules do not change their interaction parameters in response to the local molecular landscape. In this work, we propose a novel modeling strategy that involves using two rigid non-polarizable models as states that water molecules can adopt depending on their molecular environment. During the simulation, molecules dynamically transition from one state to another depending on a local order parameter that quantifies some local structural feature. In particular, molecules belonging to low- and high-tetrahedral order environments are represented with the TIP4P/2005 and TIP4P/Ice rigid models, respectively. In this way, the interaction between water molecules is strengthened when they acquire a tetrahedral coordination, which can be viewed as an effective way of introducing polarization effects. We call the resulting model TIP4P2005Ice and show that it outperforms either of the rigid models that build it. This multi-state strategy only slows down simulations by a factor of 1.5 compared to using a standard non-polarizable model and holds great promise for improving simulations of water and aqueous solutions.

Hydroxyurea inhibits proliferation and stimulates apoptosis through inducible nitric oxide synthase in erythroid cells

Hydroxyurea (hydroxycarbamide, HU) arrests cells in the S-phase by inhibiting ribonucleotide reductase and DNA synthesis, significantly contributing to the release of nitric oxide (NO). We investigated the involvement of inducible NO synthase (NOS2) in the cytostatic effect of HU using in vitro shRNA-induced knockdown of the NOS2 transcript (NOS2kd) or a specific NOS2 inhibitor (1400W) in human erythroleukemic HEL92.1.7 cells, as well as murine erythroid progenitors (mERPs) from HU-treated wild-type (WT) and Nos2 knockout (Nos2-/-) mice. Over the long-term, HU increased NOS2 expression in HEL92.1.7 cells (via nuclear factor kappa B [NFκB] signaling) and in mERP. In the short-term, HU increased the activity of human recombinant and erythroleukemic cell-derived NOS2, as confirmed by NO metabolite nitrite/citrulline production. In silico molecular docking predicted that HU binds to the NOS2 active site and substrate L-arginine via hydrogen bonds. Molecular dynamics simulations showed reduced rigidity of the NOS2 active site upon interaction with HU, indicating stabilization of the enzyme-substrate complex. Both 1400W and NOS2kd prevented the in vitro reduction in proliferation and induction of apoptosis in HEL92.1.7 cells by HU. NOS2kd preferentially blocked early apoptosis and HU-induced S-phase arrest in HEL92.1.7 cells. The HU-induced decrease in proliferation and stimulation of early apoptosis in mERP were prevented in Nos2-/- mice and by 1400W in WT mice. This study demonstrated that HU induces NOS2 activity through direct interaction and increased protein expression via NFκB signaling. Moreover, NOS2 mediates the HU-induced inhibition of proliferation and stimulation of apoptosis in erythroid cells.

Molecularly imprinted polymer-based sensors for identification volatile compounds in pharmaceutical products: in silico rational design

The present study aimed to strategically design a Molecularly Imprinted Polymer (MIP) with selective extraction capabilities for volatile compounds found in pork. These specific volatile compounds, such as 3-methyl-1-butanol, 1-nonanal, octanal, hexanal, 2-pentyl-furan, 1-penten-3-one, N-morpholinomethyl-isopropyl-sulfide, methyl butyrate, and (E,E)-2,4-decadienal, are primarily responsible for the distinctive aroma and flavor characteristics associated with pork. Molecular dynamics simulations were employed to investigate the stability of the pre-polymerization system, simulating the interactions between the volatile compounds as templates, 4-hydroxyethyl methacrylate (HEMA) as monomers, and ethylene glycol dimethacrylate (EGDMA) as crosslinkers. Computational simulations revealed that the optimal mole ratio of 1:4:20 for templates, monomers, and crosslinkers resulted in the most favorable functional radial distribution and exhibited the strongest interactions. To validate the computational findings, additional analyses were performed utilizing Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA), radial distribution function (RDF), and hydrogen bond (HBond) occupancy. The calculated binding free energy demonstrated that all template molecules were capable to bind with both the monomers and crosslinkers, including 1-penten-3-one and N-morpholinomethyl-isopropyl-sulfide displaying the strongest interactions, with values of -12,674 kJ/mol and -11,646 kJ/mol, respectively. The congruence between the results obtained from the molecular simulation analyses highlights the crucial role of molecular dynamics simulations in the study and development of MIP for the analysis of marker compounds present in pork.Communicated by Ramaswamy H. Sarma.

Extension of the lattice-based aggregation-volume-bias Monte Carlo approach to molecular crystals: Quantitative calculations on the thermodynamic stability of the urea polymorphs

Motivated by the recent success in using a latticed-based version of the aggregation-volume-bias Monte Carlo method to determine the thermodynamic stabilities of both bcc and fcc clusters formed by Lennard-Jones particles, this approach is extended to the calculation of the nucleation-free energies of solid clusters formed by urea at 300 K in two different polymorphs, i.e., form I and form IV. In addition to the lattice confinement, the constraint on the molecular orientation was found necessary to ensure that the clusters sampled in these simulations are in the corresponding form. A model that can reproduce the experimental properties such as density and lattice parameters of form I at ambient conditions is used in this study. From the size dependencies of the free energies obtained for a finite set of clusters studied, the free energies of clusters at other sizes, including an infinitely large cluster, were extrapolated. At the infinite size, equivalent to a bulk solid, form I was found to be more stable than form IV, which agrees with the experimental results. In addition, form I was found to be thermodynamically stable throughout the entire cluster size range investigated here, which contradicts the previous finding that small form I clusters are unstable from the crystal nucleation simulation studies.

Predicting anti-COVID-19 potential: in silico analysis of Mauritine compound from Ziziphus-spina christi as a promising papain-like protease (PLpro) inhibitor

The COVID-19 pandemic caused by the SARS-CoV-2 virus, recognized by the World Health Organization (WHO), has led to 164,523,894 confirmed cases and 3,412,032 deaths globally as of May 20, 2021. SARS-CoV-2 encodes crucial proteases for its replication cycle, including the papain-like protease (PLpro), presenting a potential target for developing COVID-19 treatments. Mauritine, a cyclopeptide alkaloid found in the Ziziphus-spina christi plant, exhibits antiviral properties and was investigated for its affinity and toxicity towards PLpro using molecular docking through MGLTools 1.5.6 with Autodock Tools 4.2. Preceding this, toxicity and ADME prediction were performed via Toxtree 3.1.0 software and SwissADME servers. Results from molecular docking revealed free binding energy values of -8.58; -7.73; -8.36; -6.07; -6.67; -7.83; -7.67; -7.40; and -6.87 Kcal/mol for Mauritine-A, Mauritine-B, Mauritine-C, Mauritine-D, Mauritine-F, Mauritine-H, Mauritine-J, Mauritine-L, and Mauritine-M, respectively. Correspondingly, inhibition constants were 0.51724; 2.14; 0.7398; 35.43; 12.95; 1.83; 2.38; 3.80; and 9.17 µM, respectively. Interactions observed included hydrogen bonds, hydrophobic interactions, and electrostatic interactions between the Mauritine compounds and the receptor. Mauritine-A and Mauritine-C emerged as a promising anti-COVID-19 candidate due to its superior affinity compared to other derivatives, as indicated by research findings. Interestingly, Mauritine-A and Mauritine-C exhibits notable stability as depicted by the RMSD and RMSF graphs, along with a considerable MM-PBSA binding free energy value of -162.431 and -137.500 kJ/mol, respectively.

Sensitivity of solid phase stability to the interparticle potential range: studies of a new Lennard-Jones like model

In a recent article, Wang et al. (Phys. Chem. Chem. Phys., 2020, 22, 10624) introduced a new class of interparticle potential for molecular simulations. The potential is defined by a single range parameter, eliminating the need to decide how to truncate truly long-range interactions like the Lennard-Jones (LJ) potential. The authors explored the phase diagram for a particular value of the range parameter for which their potential is similar in shape to the LJ 12-6 potential. We have reevaluated the solid phase behaviour of this model using both Lattice Switch Monte Carlo and thermodynamic integration. In addition to finding that the boundary between hexagonal close packed (hcp) and face centred cubic (fcc) phases presented by Wang et al. was calculated incorrectly, we show that owing to its finite range, the new potential exhibits several reentrant transitions between hcp and fcc phases. These phases, which do not occur in the full (untruncated) LJ system, are also found for typically adopted forms of the truncated and shifted LJ potential. However, whilst in the latter case one can systematically investigate and correct for the effects of the finite range on the calculated phase behaviour (a correction beyond the standard long-range mean field tail correction being required), this is not possible for the new potential because the choice of range parameter affects the entire potential shape. Our results highlight that potentials with finite range may fail to represent the crystalline phase behavior of systems with long-range dispersion interactions, even qualitatively.

Effectiveness of sesquiterpene derivatives from Cinnamomum genus in nicotine replacement therapy through blocking acetylcholine nicotinate: a computational analysis

Cigarette smoking poses various health risks, such as increasing the susceptibility to respiratory infections, contributing to osteoporosis, causing reproductive issues, delaying postoperative recovery, promoting ulcer formation and heightening the risk of diabetes. While many harmful effects of smoking are attributed to other cigarette components, it is nicotine's pharmacological effects that underlie tobacco addiction. Nicotine replacement therapy (NRT) aims to alleviate the urge to smoke and mitigate physiological and psychomotor withdrawal symptoms by delivering nicotine. This study explores the potential of sesquiterpene derivative compounds derived from the Cinnamomum genus using computational techniques. The research incorporates molecular docking analyses, Lipinski's rule of five filtration for drug-likeness, pharmacokinetic and toxicity predictions to assess safety profiles and molecular dynamics (MD) simulations to gauge interaction stability. The findings reveal that all sesquiterpene derivative compounds from the Cinnamomum genus can potentially inhibit nicotinic acetylcholine receptors (nAChRs), particularly nAChRÿ7. However, only abscisic acid exhibit active inhibition, along with suitable drug properties, pharmacokinetics and toxicity profiles. MD studies confirm the stability of interactions between abscisic acid with nAChRÿ7. Consequently, abscisic acid, as sesquiterpene derivatives from the Cinnamomum genus, holds substantial promise for further investigation as nAChRÿ7 inhibitors.Communicated by Ramaswamy H. Sarma.

A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals

Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.

Inhibition mechanism of membrane-separated silver carp hydrolysates on ice crystal growth obtained through experiments and molecular dynamics simulation

The membrane-separated silver carp hydrolysates (>10 k_D, 3-10 k_D and < 3 k_D) displayed abilities to mitigate oxidation and denaturation of myofibrillar protein and cryoprotective activities for frozen surimi. However, the mechanism of the membrane-separated fractions on ice crystal growth in the system is still unknown. Therefore, the cryoprotective activities (recrystallization inhibition, RI and thermal hysteresis activity, THA) of the fractions were investigated and the mechanism was explored by molecular dynamics (MD) simulation to predict the probable binding sites and model the possible interactions between the peptides and water/ice. The fractions < 3 k_D displayed remarkable RI activity, with significantly higher THA (0.60 ± 0.13 °C) and lower amount of ice nuclei (4.74 ± 0.53%) than that of fractions > 10 k_D and 3-10 k_D. The results of MD simulation certified that the main peptides in the fractions < 3 k_D interacted firmly with water molecules and inhibited growth of ice crystals with mechanism compatible with Kelvin effect. Hydrophilic and hydrophobic amino acid residues in the membrane-separated fractions offered synergistic effects on the inhibition of ice crystals.

Structure and proposed DNA delivery mechanism of a marine roseophage

Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.

Role of Crystal Disorder and Mechanoactivation in Solid-State Stability of Pharmaceuticals

Common energy-intensive processes applied in oral solid dosage development, such as milling, sieving, blending, compaction, etc. generate particles with surface and bulk crystal disorder. An intriguing aspect of the generated crystal disorder is its evolution and repercussion on the physical- and chemical stabilities of drugs. In this review, we firstly examine the existing literature on crystal disorder and its implications on solid-state stability of pharmaceuticals. Secondly, we discuss the key aspects related to the generation and evolution of crystal disorder, dynamics of the disordered/amorphous phase, analytical techniques to measure/quantify them, and approaches to model the disordering propensity from first principles. The main objective of this compilation is to provide special impetus to predict or model the chemical degradation(s) resulting from processing-induced manifestation in bulk solid manufacturing. Finally, a generic workflow is proposed that can be useful to investigate the relevance of crystal disorder on the degradation of pharmaceuticals during stability studies. The present review will cater to the requirements for developing physically- and chemically stable drugs, thereby enabling early and rational decision-making during candidate screening and in assessing degradation risks associated with formulations and processing.

Phase diagrams-Why they matter and how to predict them

Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.

Can molecular simulations reliably compare homogeneous and heterogeneous ice nucleation?

In principle, the answer to the posed titular question is undoubtedly "yes." But in practice, requisite reference data for homogeneous systems have been obtained with a treatment of intermolecular interactions that is different from that typically employed for heterogeneous systems. In this article, we assess the impact of the choice of truncation scheme when comparing water in homogeneous and inhomogeneous environments. Specifically, we use explicit free energy calculations and a simple mean field analysis to demonstrate that using the "cut-and-shift" version of the Lennard-Jones potential (common to most simple point charge models of water) results in a systematic increase in the melting temperature of ice I_h. In addition, by drawing an analogy between a change in cutoff and a change in pressure, we use existing literature data for homogeneous ice nucleation at negative pressures to suggest that enhancements due to heterogeneous nucleation may have been overestimated by several orders of magnitude.

Freezing point depression of salt aqueous solutions using the Madrid-2019 model

Salt aqueous solutions are relevant in many fields, ranging from biological systems to seawater. Thus, the availability of a force-field that is able to reproduce the thermodynamic and dynamic behavior of salt aqueous solutions would be of great interest. Unfortunately, this has been proven challenging, and most of the existing force-fields fail to reproduce much of their behavior. In particular, the diffusion of water or the salt solubility are often not well reproduced by most of the existing force-fields. Recently, the Madrid-2019 model was proposed, and it was shown that this force-field, which uses the TIP4P/2005 model for water and non-integer charges for the ions, provides a good description of a large number of properties, including the solution densities, viscosities, and the diffusion of water. In this work, we assess the performance of this force-field on the evaluation of the freezing point depression. Although the freezing point depression is a colligative property that at low salt concentrations depends solely on properties of pure water, a good model for the electrolytes is needed to accurately predict the freezing point depression at moderate and high salt concentrations. The coexistence line between ice and several salt aqueous solutions (NaCl, KCl, LiCl, MgCl₂, and Li₂SO₄) up to the eutectic point is estimated from direct coexistence molecular dynamics simulations. Our results show that this force-field reproduces fairly well the experimentally measured freezing point depression with respect to pure water freezing for all the salts and at all the compositions considered.

Umbrella Sampling Simulations of Carbon Nanoparticles Crossing Immiscible Solvents

We use molecular dynamics to compute the free energy of carbon nanoparticles crossing a hydrophobic–hydrophilic interface. The simulations are performed on a biphasic system consisting of immiscible solvents (i.e., cyclohexane and water). We solvate a carbon nanoparticle into the cyclohexane layer and use a pull force to drive the nanoparticle into water, passing over the interface. Next, we accumulate a series of umbrella sampling simulations along the path of the nanoparticle and compute the solvation free energy with respect to the two solvents. We apply the method on three carbon nanoparticles (i.e., a carbon nanocone, a nanotube, and a graphene nanosheet). In addition, we record the water-accessible surface area of the nanoparticles during the umbrella simulations. Although we detect complete wetting of the external surface of the nanoparticles, the internal surface of the nanotube becomes partially wet, whereas that of the nanocone remains dry. This is due to the nanoconfinement of the particular nanoparticles, which shields the hydrophobic interactions encountered inside the pores. We show that cyclohexane molecules remain attached on the concave surface of the nanotube or the nanocone without being disturbed by the water molecules entering the cavity.

Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ

Nuclear receptor REV-ERBβ is an overexpressed oncoprotein that has been used as a target for cancer treatment. The metal-complex nature of its ligand, iron protoporphyrin IX (Heme), enables the REV-ERBβ to be used for multiple therapeutic modalities as a photonuclease, a photosensitizer, or a fluorescence imaging agent. The replacement of iron with cobalt as the metal center of protoporphyrin IX changes the ligand from an agonist to an antagonist of REV-ERBβ. The mechanism behind that phenomenon is still unclear, despite the availability of crystal structures of REV-ERBβ in complex with Heme and cobalt protoporphyrin IX (CoPP). This study used molecular dynamic simulations to compare the effects of REV-ERBβ binding to Heme and CoPP, respectively. The initial poses of Heme and CoPP in complex with agonist and antagonist forms of REV-ERBβ were predicted using molecular docking. The binding energies of each ligand were calculated using the MM/PBSA method. The computed binding affinity of Heme to REV-ERBβ was stronger than that of CoPP, in agreement with experimental results. CoPP altered the conformation of the ligand-binding site of REV-ERBβ, disrupting the binding site for nuclear receptor corepressor, which is required for REV-ERBβ to regulate the transcription of downstream target genes. Those results suggest that a subtle change in the metal center of porphyrin can change the behavior of porphyrin in cancer cell signaling. Therefore, modification of porphyrin-based agents for cancer therapy should be conducted carefully to avoid triggering unfavorable effects.

Free energies of crystals computed using Einstein crystal with fixed center of mass and differing spring constants

Free energies of crystals computed using a center of mass constraint require a finite-size correction, as shown in previous work by Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)]. Their reference system is an Einstein crystal with equal spring constants. In this paper, we extend the work of Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)] to the case of differing spring constants. The generalization is convenient for constraining the center of mass in crystals with atoms of differing masses, and it helps to optimize the free energy calculations. To test the theory, we compare the free energies of LiI and NaCl crystals from calculations with differing spring constants to those computed using equal spring constants. Using these center of mass finite size corrections, we compute the true free energies of these crystals for different system sizes to eliminate the intrinsic finite-size effects. These calculations help demonstrate the size of these finite-size corrections relative to other contributions to the absolute free energy of the crystals.

Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides

Background

The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy.

Methods

We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution.

Results

The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB.

Conclusions

The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.

Computation of solid-fluid interfacial free energy in molecular systems using thermodynamic integration

In this article, we present two methods based on thermodynamic integration for computing solid-fluid interfacial free energy for a molecular system. As a representative system, we choose two crystal polymorphs of orcinol (5-methylbenzene-1,3-diol) as the solid phase and chloroform and nitromethane as the liquid phase. The computed values of the interfacial free energy are then used in combination with the classical nucleation theory to predict solvent induced polymorph selectivity during crystallization of orcinol from solution.

Computation of the Dissociation Temperature of TBAB Semiclathrate in an Aqueous Solution Using Molecular Simulations

Quaternary ammonium salts such as tetra-n-butyl ammonium bromide (TBAB) are known to form semiclathrate hydrates. Since they form at much milder conditions compared to gas hydrates, they have evoked much interest in development of new technologies for gas storage and gas separations. In this work, we present a method to compute the phase equilibrium of TBAB semiclathrate. The TBAB molecule is modeled using OPLS-AA and GAFF force fields and the results from simulations are compared with experimental data to determine the ability of the force fields to accurately predict the semiclathrate phase equilibria. It was observed that the OPLS-AA force field outperforms the GAFF force field in predicting the experimental phase equilibrium data.

Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates

Supramolecular aggregates of synthetic dye molecules offer great perspectives to prepare biomimetic functional materials for light-harvesting and energy transport. The design is complicated by the fact that structure–property relationships are hard to establish, because the molecular packing results from a delicate balance of interactions and the excitonic properties that dictate the optics and excited state dynamics, in turn sensitively depend on this packing. Here we show how an iterative multiscale approach combining molecular dynamics and quantum mechanical exciton modeling can be used to obtain accurate insight into the packing of thousands of cyanine dye molecules in a complex double-walled tubular aggregate in close interaction with its solvent environment. Our approach allows us to answer open questions not only on the structure of these prototypical aggregates, but also about their molecular-scale structural and energetic heterogeneity, as well as on the microscopic origin of their photophysical properties. This opens the route to accurate predictions of energy transport and other functional properties.

Multiscale modeling resolves the molecular structure of a synthetic light-harvesting complex, unraveling the microscopic origin of its photophysical properties.

Solubility prediction for a soluble organic molecule via chemical potentials from density of states

While the solubility of a substance is a fundamental property of widespread significance, its prediction from first principles (starting from only the knowledge of the molecular structure of the solute and solvent) remains a challenge. Recently, we proposed a robust and efficient method to predict the solubility from the density of states of a solute-solvent system using classical molecular simulation. The efficiency, and indeed the generality, of the method has now been enhanced by extending it to calculate solution chemical potentials (rather than probability distributions as done previously), from which solubility may be accessed. The method has been employed to predict the chemical potential of Form 1 of urea in both water and methanol for a range of concentrations at ambient conditions and for two charge models. The chemical potential calculations were validated by thermodynamic integration with the two sets of values being in excellent agreement. The solubility determined from the chemical potentials for urea in water ranged from 0.46 to 0.50 mol kg^-1, while that for urea in methanol ranged from 0.62 to 0.85 mol kg^-1, over the temperature range 298-328 K. In common with other recent studies of solubility prediction from molecular simulation, the predicted solubilities differ markedly from experimental values, reflecting limitations of current forcefields.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations.  We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation.    Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.

Free Energy of Classical Molecular Crystals by Thermodynamic Integration from a Harmonic Reference

We develop an algorithm for calculating the normal modes of vibration of mechanical systems with constraints, particularly of molecules with rigid bonds and models of rigid molecules, and use it to obtain the harmonic free energy of a crystal. The anharmonic correction is then calculated by the conventional thermodynamic integration over temperature in the NVT ensemble. Attention is paid to finite-size errors, tail corrections, thermostat choice, ergodicity, and other sources of inaccuracies. The calculated free energy of ice XIV modeled by the TIP4P/2005 potential agrees with the previously reported value and is by one order more accurate.

Computational methodology for solubility prediction: Application to sparingly soluble organic/inorganic materials

The solubility of a crystalline material can be estimated from the absolute free energy of the solid and the excess solvation free energy. In the earlier work, we presented a general-purpose molecular-dynamics-based methodology enabling solubility predictions of crystalline compounds, yielding accurate estimates of the aqueous solubilities of naphthalene at various pressures and temperatures. In the present work, we investigate a number of prototypical complex materials, including phenanthrene, calcite, and aragonite over a range of temperatures and pressures. Our results provide stronger evidence for the power of the methodology for universal solubility predictions.

Computational methodology for solubility prediction: Application to the sparingly soluble solutes

The solubility of a crystalline substance in the solution can be estimated from its absolute solid free energy and excess solvation free energy. Here, we present a numerical method, which enables convenient solubility estimation of general molecular crystals at arbitrary thermodynamic conditions where solid and solution can coexist. The methodology is based on standard alchemical free energy methods, such as thermodynamic integration and free energy perturbation, and consists of two parts: (1) systematic extension of the Einstein crystal method to calculate the absolute solid free energies of molecular crystals at arbitrary temperatures and pressures and (2) a flexible cavity method that can yield accurate estimates of the excess solvation free energies. As an illustration, via classical Molecular Dynamic simulations, we show that our approach can predict the solubility of OPLS-AA-based (Optimized Potentials for Liquid Simulations All Atomic) naphthalene in SPC (Simple Point Charge) water in good agreement with experimental data at various temperatures and pressures. Because the procedure is simple and general and only makes use of readily available open-source software, the methodology should provide a powerful tool for universal solubility prediction.

Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

The solubility of NaCl in water is evaluated by using three force field models: Joung-Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.

Modeling Polymorphic Molecular Crystals with Electronic Structure Theory

Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.

Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model

Several methods are used in sequence to determine the chemical potential of atomistic RDX in the solid and liquid phases, and its corresponding melting point. Results yield the thermodynamic melting point of 488.75 K at 1.0 atm.

Hypoglycemic effect and mechanism of honokiol on type 2 diabetic mice

BACKGROUND

Honokiol is one of the main bioactive constituents of the traditional Chinese herbal drug Magnolia bark (Cortex Magnoliae officinalis, Hou Po). The aim of this study was to probe its anti-type 2 diabetes mellitus effects and the underlying mechanism.

METHODS

Type 2 diabetic mouse model was established by intraperitoneally injecting with streptozotocin. Fasting blood glucose, body weight, and lipid profile were measured. The subcutaneous adipose tissue, skeletal muscle, and liver were isolated as well as homogenized. The phospho-insulin receptor β-subunit (IRβ), IRβ, phospho-AKT, AKT, phospho-ERK1/2, ERK1/2, phosphotyrosine, and actin were examined by Western blot assay. Cell viability or cytotoxicity was analyzed by using MTT method. The inhibitory potencies of honokiol on the protein tyrosine phosphatase 1B (PTP1B) activity were performed in reaction buffer. Molecular docking and dynamic simulation were also analyzed.

RESULTS

In in vivo studies, oral treatment with 200 mg/kg honokiol for 8 weeks significantly decreases the fasting blood glucose in type 2 diabetes mellitus mice. The phosphorylations of the IRβ and the downstream insulin signaling factors including AKT and ERK1/2 significantly increase in adipose, skeletal muscle, and liver tissue of the honokiol-treated mice. Moreover, honokiol enhanced the insulin-stimulated phosphorylations of IRβ, AKT, and ERK1/2 in a dose-dependent manner in C2C12 myotube cells. Meanwhile, honokiol enhanced insulin-stimulated GLUT4 translocation. Importantly, honokiol exhibited reversible competitive inhibitory activity against PTP1B with good selectivity in vitro and in vivo. Furthermore, using molecular docking and dynamic simulation approaches, we determined the potential binding mode of honokiol to PTP1B at an atomic level.

CONCLUSION

These findings indicated the hypoglycemic effects of honokiol and its mechanism that honokiol improved the insulin sensitivity by targeting PTP1B. Therefore, our study may highlight honokiol as a promising insulin sensitizer for the therapy of type 2 diabetes.

A unified approach to computation of solid and liquid free energy to revisit the solid-fluid equilibrium of Lennard-Jones chains

Liquid free energies are computed by integration along a path from a reference system of known free energy, using a strong localization potential. A particular choice of localization pathway is introduced, convenient for use in molecular dynamics codes, and which achieves accurate results without the need to include the identity-swap or relocation Monte Carlo moves used in previous studies. Moreover, an adaptive timestep is introduced to attain the reference system. Furthermore, a center-of-mass correction that is different from previous studies and phase-independent is incorporated. The resulting scheme allows computation of both solid and liquid free energies with only minor differences in simulation protocol. This is used to re-visit solid-liquid equilibrium in a system of short semi-flexible Lennard-Jones chain molecules. The computed melting curve is demonstrated to be consistent with direct co-existence simulations and computed hysteresis loops, provided that an entropic term arising from unsampled solid states is included.

Phase diagram of inverse patchy colloids assembling into an equilibrium laminar phase

We numerically study the phase behavior of colloidal particles with two charged patches at the poles and an oppositely charged equatorial belt. Interactions between particles are described using the inverse patchy colloid model, where the term inverse emphasizes the difference with respect to conventional patchy particles: as a consequence of the heterogeneous charge distribution, the patches on the particle surface repel each other, whereas the patches and non-patch regions mutually attract. For the model parameters considered in this work, the system exhibits an unusual equilibrium phase diagram characterized by a broad region where a novel structure composed of parallel colloidal monolayers is stable.

On fluid-solid direct coexistence simulations: the pseudo-hard sphere model

We investigate methodological issues concerning the direct coexistence method, an increasingly popular approach to evaluate the solid-fluid coexistence by means of computer simulations. The first issue is the impact of the simulation ensemble on the results. We compare the NpT ensemble (easy to use but approximate) with the NpzT ensemble (rigorous but more difficult to handle). Our work shows that both ensembles yield similar results for large systems (>5000 particles). Another issue, which is usually disregarded, is the stochastic character of a direct coexistence simulation. Here, we assess the impact of stochasticity in the determination of the coexistence point. We demonstrate that the error generated by stochasticity is much larger than that caused by the use of the NpT ensemble, and can be minimized by simply increasing the system size. To perform this study we use the pseudo hard-sphere model recently proposed by Jover et al. [J. Chem. Phys. 137, 144505 (2012)], and obtain a coexistence pressure of p∗ = 11.65(1), quite similar to that of hard spheres (only about 0.6% higher). Therefore, we conclude that this model can be reliably used to investigate the physics of hard spheres in phenomena like crystal nucleation.