DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields.

Preparing input files for molecular dynamics (MD) simulations can be a tedious task, particularly if different MD programs need to be used. Most simulation packages are accompanied by applications that handle this task, and, in some cases, software to perform interconversion between MD programs can be found. However, the conversion between different types of files is not always foolproof or the force field may not be fully supported, as quite often observed with polarization models. This work describes the program DLPGEN, which produces input files for the MD programs GROMACS, CHARMM, DL_POLY, and LAMMPS. The program can prepare polarizable force fields using a self-consistent field approach or with a dual thermostat-extended Lagrangian model. For GROMACS, a new polarization scheme suitable for the simulation of molecules containing more than one virtual particle is described. Results obtained for ethanol in the liquid state revealed that the system configurational energy, liquid density, and self-diffusion coefficient obtained with GROMACS are in good agreement with the data found with LAMMPS and CHARMM. In the case of DL_POLY, a problem with the Shells temperature control was found, suggesting that this program may not be suitable for the simulation of molecules containing multiple Drude particles.

The Solubility of Gases in Ionic Liquids: A Chemoinformatic Predictive and Interpretable Approach.

This work comprises the study of solubilities of gases in ionic liquids (ILs) using a chemoinformatic approach. It is based on the codification, of the atomic inter-component interactions, cation/gas and anion/gas, which are used to obtain a pattern of activation in a Kohonen Neural Network (MOLMAP descriptors). A robust predictive model has been obtained with the Random Forest algorithm and used the maximum proximity as a confidence measure of a given chemical system compared to the training set. The encoding method has been validated with molecular dynamics. This encoding approach is a valuable estimator of attractive/repulsive interactions of a generical chemical system IL+gas. This method has been used as a fast/visual form of identification of the reasons behind the differences observed between the solubility of CO2 and O2 in 1-butyl-3-methylimidazolium hexafluorophosphate (BMIM PF6 ) at identical temperature and pressure (TP) conditions, The effect of variable cation and anion effect has been evaluated.

First and Second Dissociation Enthalpies in Bi-Component Crystals Consisting of Maleic Acid and L-Phenylalanine.

The energetics of the stepwise dissociation of a A:B2 bi-component crystal, according to A:B2(cr) → A:B(cr) + B(cr) and A:B(cr) → A(cr) + B(cr), was investigated using MA:Phe2 and MA:Phe (MA = maleic acid; Phe = L-phenylalanine) as model systems. The enthalpy changes associated with these sequential processes and with the overall dissociation reaction A:B2(cr) → A(cr) + 2B(cr) were determined by solution calorimetry. It was found that they are all positive, indicating that there is a lattice enthalpy gain when MA:Phe2 is formed, either from the individual precursors or by adding Phe to MA:Phe. Single-crystal X-ray diffraction (SCXRD) analysis showed that MA:Phe2 is best described as a protic salt containing a maleate anion (MA-) and two non-equivalent L-phenylalanine units, both linked to MA- by NH···O hydrogen bonds (H-bond): one of these units is protonated (HPhe+) and the other zwitterionic (Phe±). Only MA- and HPhe+ molecules are present in the MA:Phe lattice. In this case, however, NH···O and OH···O H-bonds are formed between each MA- unit and two HPhe+ molecules. Despite these structural differences, the enthalpy cost for the removal of the zwitterionic Phe± unit from the MA:Phe2 lattice to yield MA:Phe is only 0.9 ± 0.4 kJ mol-1 higher than that for the dissociation of MA:Phe, which requires a proton transfer from HPhe+ to MA- and the rearrangement of L-phenylalanine to the zwitterionic, Phe±, form. Finally, a comparison of the dissociation energetics and structures of MA:Phe and of the previously reported glycine maleate (MA:Gly) analogue indicated that parameters, such as the packing coefficient, density, hydrogen bonds formed, or fusion temperature, are not necessarily good descriptors of dissociation enthalpy or lattice enthalpy trends when bi-component crystals with different molecular composition are being compared, even if the stoichiometry is the same.

C13 - a new empirical force field to characterize the mechanical behavior of carbyne chains.

An accurate prediction of the mechanical behavior of long carbyne chains depends on the suitable modeling of bond alternation in these chains. While first-principles methods are a good approach, less computationally demanding empirical potentials are preferable for large carbyne-containing systems. AIREBO and Reax empirical potentials have extensively and successfully been used for simulating the mechanical behavior of graphene and carbon nanotubes. However, it remains unclear if these potentials can be directly applied in the accurate mechanical modeling of carbon nanostructures with sp hybridization, without re-parameterization. Here, a new force-field for carbyne, designated as C13 potential, that takes bond alternation into account, is presented. This new empirical potential was parameterized from ab initio calculations. Molecular dynamics (MD) simulations using the developed force-field are then conducted to determine the mechanical properties of carbyne chains under tensile loading, namely to assess their dependence on chain length and temperature. The bending stiffness of carbyne and its persistence length are also calculated. The results obtained are validated through comparison with results available in the literature. Lastly, the C13 potential is employed to model, for the first time, the tensile and the compressive behaviors of the hybrid system composed of carbon nanotubes infilled with carbyne chains.

Tuning the miscibility of water in imide-based ionic liquids.

Liquid-liquid phase behavior measurements were performed for binary mixtures of water and ionic liquids (ILs) containing the same 1-ethyl-3-methylimidazolium ([C2mim]+) cation and different imide-based anions, having symmetric (bis(fluorosulfonyl)imide ([FSI]-)) or asymmetric structures (2,2,2-trifluoromethylsulfonyl-N-cyanoamide ([TFSAM]-) and 2,2,2-trifluoro-N-(trifluoromethylsulfonyl)acetamide ([TSAC]-)). An inversion of phase behavior was observed: while below ∼298 K, the miscibility of water in the studied ILs increases according to the order [C2mim][TSAC] < [C2mim][FSI] < [C2mim][NTf2], for temperatures above ∼303 K, the reverse trend is observed [C2mim][NTf2] < [C2mim][FSI] < [C2mim][TSAC]. In turn, above ∼306 K the [C2mim][TFSAM] is completely miscible with H2O in all ranges of concentrations. The obtained results also revealed an unusual water solubility variation of 11% in [C2mim][FSI], and 20% in [C2mim][TSAC], when the system temperature was changed by less than 1 K, around 298 K and 301 K, respectively. Molecular Dynamics (MD) simulations were used to understand the IL-water interactions and rationalize the experimental observations. These results suggested that the miscibility trends are mainly related to the ability of the water molecules to form water-anion and water-water aggregates in solution.

Neat ionic liquids versus ionic liquid mixtures: a combination of experimental data and molecular simulation.

Simple mixtures of ionic liquids (IL-IL mixtures) can become a promising approach for the substitution of task-specific ILs. Such a concept was explored in this article by comparison of the thermophysical properties of neat 1-ethyl-3-methylimidazolium 2,2,2-trifluoromethylsulfonyl-N-cyanoamide, [C2mim][TFSAM], and equimolar mixtures of two structurally similar ILs having more common ions. Molecular dynamics (MD) simulations were additionally used to further highlight structural aspects of these systems at a molecular level.

Polymorphism in Simvastatin: Twinning, Disorder, and Enantiotropic Phase Transitions.

Simvastatin is one of the most widely used active pharmaceutical ingredients for the treatment of hyperlipidemias. Because the compound is employed as a solid in drug formulations, particular attention should be given to the characterization of different polymorphs, their stability domains, and the nature of the phase transitions that relate them. In this work, the phase transitions delimiting the stability domains of three previously reported simvastatin forms were investigated from structural, energetics, and dynamical points of view based on single crystal X-ray diffraction (SCXRD), hot stage microscopy (HSM), and differential scanning calorimetry (DSC) experiments (conventional scans and heat capacity measurements), complemented with molecular dynamics (MD) simulations. Previous assignments of the crystal forms were confirmed by SCXRD: forms I and II were found to be orthorhombic ( P212121, Z'/ Z = 1/4) and form III was monoclinic ( P21, Z'/ Z = 2/4). The obtained results further indicated that (i) the transitions between different forms are observed at 235.9 ± 0.1 K (form III → form II) and at 275.2 ± 0.2 K (form II → form I) in DSC runs carried out at 10 K min-1 and close to these values when other types of techniques are used (e.g., HSM). (ii) They are enantiotropic (i.e., there is a transition temperature relating the two phases before fusion at which the stability order is reversed), fast, reversible, with very little hysteresis between heating and cooling modes, and occur under single crystal to single crystal conditions. (iii) A nucleation and growth mechanism seems to be followed since HSM experiments on single crystals evidenced the propagation of an interface, accompanied by a change of birefringence and crystal contraction or expansion (more subtle in the case of form III → form II), when the phase transitions are triggered. (iv) Consistent with the reversible and small hysteresis nature of the phase transitions, the SCXRD results indicated that the molecular packing is very similar in all forms and the main structural differences are associated with conformational changes of the "ester tail". (v) The MD simulations further suggested that the tail is essentially "frozen" in two conformations below the III → II transition temperature, becomes progressively less hindered throughout the stability domain of form II, and acquires a large conformational freedom above the II → I transition. Finally, the fact that these transitions were found to be fast and reversible suggests that polymorphism is unlikely to be a problem for pharmaceutical formulations employing crystalline simvastatin because, if present, the III and II forms will readily convert to form I at ambient temperature.

Extraction Optimization and Structural and Thermal Characterization of the Antimicrobial Abietane 7α-Acetoxy-6ß-hydroxyroyleanone.

The abietane 7α-acetoxy-6ß-hydroxyroyleanone (AHR), obtained from plant extracts, is an attractive lead for drug development, given its known antimicrobial properties. Two basic requirements to establish any compound as a new drug are the development of a convenient extraction process and the characterization of its structural and thermal properties. In this work seven different methods were tested to optimize the extraction of AHR from Plectranthus grandidentatus. Supercritical fluid extraction (SFE) proved to be the method of choice, delivering an amount of AHR (57.351 µg·mg-1) approximately six times higher than the second best method (maceration in acetone; 9.77 µg·mg-1). Single crystal X-ray diffraction analysis of the ARH molecular and crystal structure carried out at 167 ± 2 K and 296 ± 2 K showed only a single phase, here dubbed form III (orthorhombic space group P21212), at those temperatures. The presence of two other polymorphs above room temperature was, however, evidenced by differential scanning calorimetry (DSC). The three forms are enantiotropically related, with the form III → form II and form II → form I transitions occurring at 333.5 ± 1.6 K and 352.0 ± 1.6 K, respectively. The fact that the transitions are reversible suggests that polymorphism is not likely to be an issue in the development pharmaceutical formulations based on ARH. DSC experiments also showed that the compound decomposes on melting at 500.8 ± 0.8 K. Melting should therefore be avoided if, for example, strategies to improve solubility based on the production of glassy materials or solid dispersions are considered.

Solvation of alcohols in ionic liquids - understanding the effect of the anion and cation.

In this work, we studied the effect of anion and cation properties on the interaction of alcohols with ionic liquids (ILs), using propan-1-ol as a molecular probe. The enthalpies of solution at infinite dilution of propan-1-ol in several ILs were measured by isothermal titration calorimetry (ITC). The calorimetric results were analysed together with molecular dynamics simulation and quantum chemical calculations of the interaction of the hydroxyl group of propan-1-ol with the anions. The results evidenced the role of the anion's basicity in the intermolecular interactions of alcohols and ionic liquids and further revealed a secondary effect of the cation nature on the solvation process. The effect of the anion basicity on the strength of the interaction of alcohols with ionic liquids was evaluated by comparing the results obtained for ILs with the same cation and different anions, [C4C1im][anion] (anions NTf2, PF6, FAP, DCA and TFA). The effect of the cation (size, aromaticity, charge distribution, and acidity) was explored using five different cations of the NTf2 series, [cation][NTf2] (cations C4C1im, C4C1pirr, C4py, C4C1pip, and C3C1C1im).

AGGREGATES: Finding structures in simulation results of solutions.

Molecular Dynamic and Monte-Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures. Tools designed to investigate the local organization and the molecular conformations in the clusters are also available. Among these, it is introduced a new approach to perform a First Shell Analysis, by looking for the presence of atomic contacts between molecules. These elements are particularly useful to obtain information on molecular assembly processes (such as the nucleation of crystals or colloidal particles) or to investigate polymorphism in organic compounds. The program features are illustrated here through the investigation of the 4'-hydroxyacetophenone + ethanol system. © 2017 Wiley Periodicals, Inc.

ForConX: A forcefield conversion tool based on XML.

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials. © 2017 Wiley Periodicals, Inc.

Ionic liquids with anions based on fluorosulfonyl derivatives: from asymmetrical substitutions to a consistent force field model.

Herein, seven anions including four imide-based, namely bis[(trifluoromethyl)sulfonyl]imide (TFSI), bis(fluorosulfonyl)imide (FSI), bis[(pentafluoroethyl)sulfonyl]imide (BETI), 2,2,2-trifluoromethylsulfonyl-N-cyanoamide (TFSAM) and 2,2,2-trifluoro-N-(trifluoromethylsulfonyl) acetamide (TSAC), and two sulfonate anions, trifluoromethanesulfonate (triflate, TF) and nonafluorobutanesulfonate (NF), are considered and compared. The volumetric mass density and dynamic viscosity of five ionic liquids containing these anions combined with the commonly used 1-ethyl-3-methylimidazolium cation (C2C1im), [C2C1im][FSI], [C2C1im][BETI], [C2C1im][TFSAM], [C2C1im][TSAC] and [C2C1im][NF] are measured in the temperature range of 293.15 ≤ T/K ≤ 353.15 and at atmospheric pressure. The results show that [C2mim][FSI] and [C2mim][TFSAM] exhibit the lowest densities and viscosities among all the studied ionic liquids. The experimental volumetric data is used to validate a more consistent re-parameterization of the CL&P force field for use in MD simulations of ionic liquids containing the ubiquitous bis[(trifluoromethyl)sulfonyl]imide and trifluoromethanesulfonate anions and to extend the application of the model to other molten salts with similar ions.

Structure-property relationships in protic ionic liquids: a study of solvent-solvent and solvent-solute interactions.

The ionic nature of a functionalized protic ionic liquid cannot be rationalized simply through the differences in aqueous proton dissociation constants between the acid precursor and the conjugate acid of the base precursor. The extent of proton transfer, i.e. the equilibrium ionicity, of a tertiary ammonium acetate protic ionic liquid can be significantly increased by introducing an hydroxyl functional group on the cation, compared to the alkyl or amino-functionalized analogues. This increase in apparent ionic nature correlates well with variations in solvent-solute and solvent-solvent interaction parameters, as well as with physicochemical properties such as viscosity.

Structure-property relationships in protic ionic liquids: a thermochemical study.

How does cation functionality influence the strength of intermolecular interactions in protic ionic liquids (PILs)? Quantifying the energetics of PILs can be an invaluable tool to answer this fundamental question. With this in view, we have determined the standard molar enthalpy of vaporization, , and the standard molar enthalpy of formation, , of three tertiary ammonium acetate PILs with varying cation functionality, and of their corresponding precursor amines, through a combination of Calvet-drop microcalorimetry, solution calorimetry, and ab initio calculations. The obtained results suggest that these PILs vaporize as their neutral acid and base precursors. We also found a strong correlation between of the PILs and of their corresponding amines. This suggests that, within this series of PILs, the influence of cation modification on their cohesive energies follows a group additivity rule. Finally, no correlation between the of PILs and the extent of proton transfer, as estimated from the difference in aqueous pKa between the precursor acid and the conjugate acid of the precursor base, was observed.

Additive polarizabilities in ionic liquids.

An extended designed regression analysis of experimental data on density and refractive indices of several classes of ionic liquids yielded statistically averaged atomic volumes and polarizabilities of the constituting atoms. These values can be used to predict the molecular volume and polarizability of an unknown ionic liquid as well as its mass density and refractive index. Our approach does not need information on the molecular structure of the ionic liquid, but it turned out that the discrimination of the hybridization state of the carbons improved the overall result. Our results are not only compared to experimental data but also to quantum-chemical calculations. Furthermore, fractional charges of ionic liquid ions and their relation to polarizability are discussed.

Mixtures of the 1-ethyl-3-methylimidazolium acetate ionic liquid with different inorganic salts: insights into their interactions.

In this work, we explore the interactions between the ionic liquid 1-ethyl-3-methylimidazolim acetate and different inorganic salts belonging to two different cation families, those based on ammonium and others based on sodium. NMR and Raman spectroscopy are used to screen for changes in the molecular environment of the ions in the ionic liquid + inorganic salt mixtures as compared to pure ionic liquid. The ion self-diffusion coefficients are determined from NMR data, allowing the discussion of the ionicity values of the ionic liquid + inorganic salt mixtures calculated using different methods. Our data reveal that preferential interactions are established between the ionic liquid and ammonium-based salts, as opposed to sodium-based salts. Computational calculations show the formation of aggregates between the ionic liquid and the inorganic salt, which is consistent with the spectroscopic data, and indicate that the acetate anion of the ionic liquid establishes preferential interactions with the ammonium cation of the inorganic salts, leaving the imidazolium cation less engaged in the media.

Modeling the structure and thermodynamics of ferrocenium-based ionic liquids.

A new force-field for the description of ferrocenium-based ionic liquids is reported. The proposed model was validated by confronting Molecular Dynamics simulations results with available experimental data-enthalpy of fusion, crystalline structure and liquid density-for a series of 1-alkyl-2,3,4,5,6,7,8,9-octamethylferrocenium bis(trifluoromethylsulfonyl)imide ionic liquids, [CnFc][NTf2] (3 ≤ n ≤ 10). The model is able to reproduce the densities and enthalpies of fusion with deviations smaller than 2.6% and 4.8 kJ mol(-1), respectively. The MD simulation trajectories were also used to compute relevant structural information for the different [CnFc][NTf2] ionic liquids. The results show that, unlike other ILs, the alkyl side chains present in the cations are able to interact directly with the ferrocenium core of other ions. Even the ferrocenium charged cores (with relatively mild charge densities) are able to form small contact aggregates. This causes the partial rupture of the polar network and precludes the formation of extended nano-segregated polar-nonpolar domains normally observed in other ionic liquids.

Evaluation of the OPLS-AA force field for the study of structural and energetic aspects of molecular organic crystals.

Motivated by the need for reliable experimental data for the assessment of theoretical predictions, this work proposes a data set of enthalpies of sublimation determined for specific crystalline structures, for the validation of molecular force fields (FF). The selected data were used to explore the ability of the OPLS-AA parametrization to investigate the properties of solid materials in molecular dynamics simulations. Furthermore, several approaches to improve this parametrization were also considered. These modifications consisted in replacing the original FF atomic point charges (APC), by values calculated using quantum chemical methods, and by the implementation of a polarizable FF. The obtained results indicated that, in general, the best agreement between theoretical and experimental data is found when the OPLS-AA force field is used with the original APC or when these are replaced by ChelpG charges, computed at the MP2/aug-cc-pVDZ level of theory, for isolated molecules in the gaseous phase. If a good description of the energetic relations between the polymorphs of a compound is required then either the use of polarizable FF or the use of charges determined taking into account the vicinity of the molecules in the crystal (combining the ChelpG and MP2/cc-pVDZ methods) is recommended. Finally, it was concluded that density functional theory methods, like B3LYP or B3PW91, are not advisable for the evaluation of APC of organic compounds for molecular dynamic simulations. Instead, the MP2 method should be considered.

Isotropic liquid state of cocoa butter.

The complex crystal structure of coca butter (CB) is responsible for the unique melting behavior, surface gloss, and mechanical properties of chocolate. While most studies concentrated on the crystalline state of CB, few studied the isotropic liquid state, which has a major impact on the crystallization process and the characteristics of the resulting crystals. In this study, the molecular organizations of the main CB triacylglycerols (TAGs; 1,3-dipalmitoyl-2-oleoylglycerol, palmitoyl-oleoyl-stearoylglycerol, POS, and 1,3-distearoyl-2-oleoylglycerol) were studied. The findings revealed the tunning-fork (Tf) conformation, commonly found in the crystalline state, is the least abundant in the isotropic liquid state of CB and pure TAGs. Notably, POS was found to interact with itself in CB, while its molecules with Tf conformation, although in small amounts in the mixture, tend to pair with each other at lower temperatures. These results highlight the significance of POS in CB crystallization and provide insights for developing CB alternatives.

Energetics and structure of simvastatin.

The study of structure-energetics relationships for active pharmaceutical ingredients has received considerable attention in recent years, due to its importance for the effective production and safe use of drugs. In this work the widely prescribed cholesterol-lowering drug simvastatin was investigated by combining experimental (combustion calorimetry and differential scanning calorimetry, DSC) and computational chemistry (quantum chemistry and molecular dynamics calculations) results. The studies addressed the crystalline form stable at ambient temperature (form I) and the liquid and gaseous phases. Heat capacity determinations by DSC showed no evidence of polymorphism between 293 K and the fusion temperature. It was also found that the most stable molecular conformation in the gas phase given by the quantum chemistry calculations (B3LYP-D3/cc-pVTZ) is analogous to that observed in the crystal phase. The molecular dynamics simulations correctly captured the main structural properties of the crystalline phase known from published single crystal X-ray diffraction results (unit cell dimensions and volume). They also suggested that, while preferential conformations are exhibited by the molecule in the solid at 298.15 K, these preferences are essentially blurred upon melting. Finally, the experiments and calculations led to enthalpies of formation of simvastatin at 298.15 K, in the crystalline (form I) ΔfH(m)(o) (cr I) = -1238.4 ± 5.6 kJ · mol(-1), liquid ΔfH(m)(o) (l) = -1226.4 ± 5.7 kJ · mol(-1), and gaseous ΔfH(m)(o) (g) = -1063.0 ± 7.1 kJ · mol(-1) states.