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A coarse-grained model comprising short- and long-range effective potentials, parametrized with the iterative Boltzmann inversion (IBI) method, is presented for capturing micelle formation in aqueous solutions of ionic surfactants using as a model system sodium dodecyl sulfate (SDS). In the coarse-grained (CG) model, each SDS molecule is represented as a sequence of four beads while each water molecule is modeled as a single bead. The proposed CG scheme involves ten potential energy functions: four of them describe bonded interactions and control the distribution functions of intramolecular degrees of freedom (bond lengths, valence angles, and dihedrals) along an SDS molecule while the other six account for intermolecular interactions between pairs of SDS and water beads and control the radial distribution functions. The nonbonded effective potentials between coarse-grained SDS molecules extend up to about 12 nm and capture structural and morphological features of the micellar solution both at short and long distances. The long-range component of these potentials, in particular, captures correlations between surfactant molecules belonging to different micelles and is essential to describe ordering associated with micelle formation. A new strategy is introduced for determining the effective potentials through IBI by using information (target distribution functions) extracted from independent atomistic simulations of a micellar reference system (a salt-free SDS solution at total surfactant concentration cT equal to 103 mM, temperature T equal to 300 K, and pressure P equal to 1 atm) obtained through a multiscale approach described in an earlier study. It employs several optimization steps for bonded and nonbonded interactions and a gradual parametrization of the short- and long-range components of the latter, followed by reparametrization of the bonded ones. The proposed CG model can reproduce remarkably accurately the microstructure and morphology of the reference system within only a few hours of computational time. It is therefore very promising for future studies of structural and morphological behavior of various liquid surfactant formulations. ISSN:1520-6106 ISSN:1520-5207 ISSN:1089-5647

We address the problem of the quantitative prediction of micelle formation in dilute aqueous solutions of ionic surfactants using sodium dodecyl sulfate (SDS) as a model system through a computational approach that involves three steps: (a) execution of coarse-grained simulations based on the MARTINI force field (with slightly modified parameters to afford the formation of large micelles); (b) reverse mapping of the final self-assembled coarse-grained configuration into an all-atom configuration; and (c) final relaxation of this all-atom configuration through short-time (on the order of a few tens of nanoseconds), detailed isothermal-isobaric molecular dynamics simulations using the CHARMM36 force field. For a given concentration of the solution in SDS molecules, the modified MARTINI-based coarse-grained simulations lead to the formation of large micelles characterized by mean aggregation numbers above the experimentally observed ones. However, by reintroducing the detailed chemical structure through a strategy that solves a well-defined geometric problem and re-equilibrating, these large micellar aggregates quickly dissolve to smaller ones and equilibrate to sizes that perfectly match the average micelle size measured experimentally at the given surfactant concentration. From the all-atom molecular dynamics simulations, we also deduce the surfactant diffusivity DSDS and the zero-shear rate viscosity, η0, of the solution, which are observed to compare very favorably with the few experimental values that we were able to find in the literature.

In a recent contribution, we introduced a new approach for the quantitative prediction of the micellar morphology of aqueous solutions of ionic surfactants based on coarse-grained MARTINI-type simulations followed by reverse-mapped all-atom (AA) molecular dynamics (MD) ones, using as a model system sodium dodecyl sulfate. We make use of the same approach in the present work to study the micellar structure of aqueous solutions of sodium lauryl ether sulfate (SLEnS) with the chemical structure CH3(CH2)11(OCH2CH2)nOSO3Na with a fixed number n of ethoxyl (EO) groups per surfactant molecule (n = 1, 2, 3). These surfactants are used in a wide range of industrial applications, particularly in personal and home care products, but a quick literature survey proves that a systematic study of their microstructure, micellar morphology, and equilibrium transport properties is missing. Our simulations provide predictions for the mean aggregation number of such monodisperse SLEnS solutions which are found to be in very good agreement with experimental data already reported in the literature. They also show that for a given total surfactant concentration, SLEnS molecules with a smaller number n of EO groups form, on average, larger micelles. From the reverse-mapped AA MD simulations we also compute the zero shear rate viscosity of the solution whose value is found to increase as its total concentration in SLEnS molecules increases (for a given n) or as the number n of EO groups in the surfactant increases (for a given concentration)., JPhys Materials, 4 (4)

Despite the considerable advances of molecular-thermodynamic theory of micelle growth, agreement between theory and experiment has been achieved only in isolated cases. A general theory that can provide self-consistent quantitative description of the growth of wormlike micelles in mixed surfactant solutions, including the experimentally observed high peaks in viscosity and aggregation number, is still missing. As a step toward the creation of such theory, here we consider the simplest system – nonionic wormlike surfactant micelles from polyoxyethylene alkyl ethers, CiEj. Our goal is to construct a molecular-thermodynamic model that is in agreement with the available experimental data. For this goal, we systematized data for the micelle mean mass aggregation number, from which the micelle growth parameter was determined at various temperatures. None of the available models can give a quantitative description of these data. We constructed a new model, which is based on theoretical expressions for the interfacial-tension, headgroup-steric and chain-conformation components of micelle free energy, along with appropriate expressions for the parameters of the model, including their temperature and curvature dependencies. Special attention was paid to the surfactant chain-conformation free energy, for which a new more general formula was derived. As a result, relatively simple theoretical expressions are obtained. All parameters that enter these expressions are known, which facilitates the theoretical modeling of micelle growth for various nonionic surfactants in excellent agreement with the experiment. The constructed model can serve as a basis that can be further upgraded to obtain quantitative description of micelle growth in more complicated systems, including binary and ternary mixtures of nonionic, ionic and zwitterionic surfactants, which determines the viscosity and stability of various formulations in personal-care and house-hold detergency.

Hypotheses: To correctly predict the aggregation number and size of wormlike micelles from ionic surfactants, the molecular-thermodynamic theory has to calculate the free energy per molecule in the micelle with accuracy better than 0.01 kT, which is a serious challenge. The problem could be solved if the effects of mutual confinement of micelle counterion atmospheres, as well as the effects of counterion binding, surface curvature and ionic interactions in the electric double layer (EDL), are accurately described. Theory: The electric field is calculated using an appropriate cell model, which takes into account the aforementioned effects. Expressions for the activity coefficients have been used, which vary across the EDL and describe the electrostatic, hard sphere, and specific interactions between the ions. New approach for fast numerical calculation of the electrostatic free energy is developed. Findings: The numerical results demonstrate the variation of quantities characterizing the EDL of cylindrical and spherical micelles with the rise of electrolyte concentration. The effect of activity coefficients leads to higher values of the free energy per surfactant molecule in the micelle as compared with the case of neglected ionic interactions. The results are essential for the correct prediction of the size of wormlike micelles from ionic surfactants. This study can be extended to mixed micelles of ionic and nonionic surfactants for interpretation of the observed synergistic effects., Comment: 36 pages, 6 figures, Supplementary Information: 12 pages, 1 figure

Hypotheses: The aggregation number and length of spherocylindrical (rodlike, wormlike) micelles in solutions of an ionic surfactant and salt can be predicted knowing the molecular parameters and the input concentrations of the species. This can be achieved by upgrading the quantitative molecular thermodynamic model from the previous parts of this series with an expression for the electrostatic component of micelle scission energy that is the excess free energy of the spherical endcaps with respect to the cylindrical part of the micelle. Theory: The thermodynamics of micellization is extended to the case of multicomponent system, which may contain several surfactants (both ionic and nonionic) and salts, taking into account the effect of counterion binding in the Stern layer on the micellar surface. Furthermore, the considerations are focused on a system that consists of single ionic surfactant plus salt. Findings: Excellent agreement was achieved between the theoretical model and experimental data for wormlike micelles from anionic and cationic surfactants at various concentrations of salt and temperatures. In accord with the experimental observations, at high salt concentrations, the model predicts loss of chemical equilibrium between the endcaps and cylindrical part of the wormlike micelles, which implies transition to self-assemblies of other, e.g. branched, morphology or the onset of crystallization and phase separation., Comment: 52 pages, 9 figures; Supplementary Information: 23 pages, 4 figures

Combination antibiotic therapies are clinically important in the fight against bacterial infections. However, the search space of drug combinations is large, making the identification of effective combinations a challenging task. Here, we present a computational framework that uses substructure profiles derived from the molecular structures of drugs and predicts antibiotic interactions. Using a previously published data set of 153 drug pairs, we showed that substructure profiles are useful in predicting synergy. We experimentally measured the interaction of 123 new drug pairs, as a prospective validation set for our approach, and identified 37 new synergistic pairs. Of the 12 pairs predicted to be synergistic, 10 were experimentally validated, corresponding to a 2.8-fold enrichment. Having thus validated our methodology, we produced a compendium of interaction predictions for all pairwise combinations among 100 antibiotics. Our methodology can make reliable antibiotic interaction predictions for any antibiotic pair within the applicability domain of the model since it solely requires chemical structures as an input.

Hypotheses A quantitative molecular-thermodynamic theory of the growth of giant wormlike micelles of nonionic surfactants can be developed on the basis of a generalized model, which includes the classical “phase separation” and “mass action” models as special cases. The generalized model describes spherocylindrical micelles, which are simultaneously multicomponent and polydisperse in size. Theory By analytical minimization of the free-energy functional we derived explicit expressions for the chain-extension and chain-end distribution functions in the hydrocarbon core of mixed micelles from two surfactants of different chainlengths. Findings The hydrocarbon core of a two-component micelle is divided in two regions, outer and inner, where the ends of the shorter and longer chains are located. The derived analytical expression for the chain-conformation free energy implies that the mixing of surfactants with different chainlengths is always nonideal and synergistic, i.e. it leads to decrease of the micellar free energy and to enhancement of micellization and micelle growth. The derived expressions are applicable to surfactants with different headgroups (nonionic, ionic, zwitterionic) and to micelles of different shapes (spherical, wormlike, lamellar). The results can be incorporated in a quantitative theory of the growth of giant mixed micelles in formulations with practical applications in detergency.

Hypotheses Quantitative molecular-thermodynamic theory of the growth of giant wormlike micelles in mixed nonionic surfactant solutions can be developed on the basis of a generalized model, which includes the classical “phase separation” and “mass action” models as special cases. The generalized model describes spherocylindrical micelles, which are simultaneously multicomponent and polydisperse in size. Theory The model is based on explicit analytical expressions for the four components of the free energy of mixed nonionic micelles: interfacial-tension, headgroup-steric, chain-conformation components and free energy of mixing. The radii of the cylindrical part and the spherical endcaps, as well as the chemical composition of the endcaps, are determined by minimization of the free energy. Findings In the case of multicomponent micelles, an additional term appears in the expression for the micelle growth parameter (scission free energy), which takes into account the fact that the micelle endcaps and cylindrical part have different compositions. The model accurately predicts the mean mass aggregation number of wormlike micelles in mixed nonionic surfactant solutions without using any adjustable parameters. The endcaps are enriched in the surfactant with smaller packing parameter that is better accommodated in regions of higher mean surface curvature. The model can be further extended to mixed solutions of nonionic, ionic and zwitterionic surfactants used in personal-care and house-hold detergency.

Background In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. Results camb is an R package that provides an environment for the rapid generation of quantitative Structure-Property and Structure-Activity models for small molecules (including QSAR, QSPR, QSAM, PCM) and is aimed at both advanced and beginner R users. camb's capabilities include the standardisation of chemical structure representation, computation of 905 one-dimensional and 14 fingerprint type descriptors for small molecules, 8 types of amino acid descriptors, 13 whole protein sequence descriptors, filtering methods for feature selection, generation of predictive models (using an interface to the R package caret), as well as techniques to create model ensembles using techniques from the R package caretEnsemble). Results can be visualised through high-quality, customisable plots (R package ggplot2). Conclusions Overall, camb constitutes an open-source framework to perform the following steps: (1) compound standardisation, (2) molecular and protein descriptor calculation, (3) descriptor pre-processing and model training, visualisation and validation, and (4) bioactivity/property prediction for new molecules. camb aims to speed model generation, in order to provide reproducibility and tests of robustness. QSPR and proteochemometric case studies are included which demonstrate camb's application.Graphical abstractFrom compounds and data to models: a complete model building workflow in one package. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0086-2) contains supplementary material, which is available to authorized users.

We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e. hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values., Comment: 12 pages, 4 figures, 7 tables, RevTeX 4.1

Publisher Summary Computer-aided molecular design (CAMD) has taken a large leap forward in recent years by the use of algorithms, such as neural networks for the prediction of properties of interest, and genetic algorithms that use the neural network models in the discovery and design of new peptides. These techniques are being successfully used to design novel bactericidal peptides. Neural net equations have been determined on the basis of a sound theoretical hypothesis of bactericidal activity, 29 experimental measures, carefully chosen molecular parameters, and the development of a predictive model based on these aspects. The patent aspects of the work have identified several legal issues. A justification for the approach lies within the context of the well-documented method of computer-aided molecular design. It remains to be seen whether such a mathematical approach will rest easy with the patent offers around the world that must approve the patent for grant. In the same way that any patent discloses the scientific understanding of a particular scientific endeavour, so the chapter has disclosed the model in full, as well as the precise method for development of the model.