Alkane Parameters Research Articles

Derivation of micelle size-dependent free energies of aggregation for octyl phosphocholine from molecular dynamics simulation

Molecular dynamics (MD) simulations of the zwitterionic surfactant octyl phosphocholine (OPC) in water have been performed with two force fields, both using the TraPPE united-atom alkane parameters for tailgroup-tailgroup interactions but with tailgroup-water interactions adjusted to reproduce hydration free energies for two different water models (SPC and TIP4P-2005). Micelle size distributions from a number of trajectories were analyzed using the PEACH (Partition-Enabled Analysis of Cluster Histograms) method to yield free energies of aggregation for premicelles and micelles over the full range from 2 to over 40 molecules. The dependence of free energy on aggregation number was consistent with the functional form derived from the “quasi-droplet” model of micellization. Free energies of aggregation were used to calculate concentration-dependent micelle size distributions, from which critical micelle concentrations (cmc's) could be inferred. The cmc values derived from PEACH free energies for the SPC and TIP4P-2005 models were 40% and 27% higher respectively than the experimentally reported value of 114 mM. In systems with enough monomers to form multiple micelles, the micelles tended to stick together, complicating the analysis. Micelle size distributions were used to weight small-angle X-ray scattering (SAXS) form factors derived from micelle structures, generating a composite form factor reflecting the polydispersity of aggregate sizes with contributions in the range from 20 to 45 monomers. The composite scattering profile was quite similar to that of the mass-weighted average micelle size, suggesting that SAXS profiles for small micelles can be adequately fit using a single typical micelle even in the presence of significant polydispersity.

Fully atomistic molecular‐mechanical model of liquid alkane oils: Computational validation

Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

Methods for Calculating the Critical Constants of Hydrocarbons (Using the n-Alkane Series as an Example)

This paper presents the calculation method allowing one to obtain the matched magnitudes of critical parameters of hydrocarbon gases with an accuracy comparable to the errors of the experimental methods. The ratios obtained allow an assessment of the values of the critical temperature, critical pressure, critical volume, acentric factor, and compressibility in the homologous series of alkanes up to C100. The critical parameters for alkanes 4 < nC < 40 calculated using formulas presented in the article demonstrated good consistency with the experimental data. The proposed values of critical constants for normal alkanes can be used to calculate the physiochemical properties of the compounds, while the calculation methods can be used to determine the critical constants of hydrocarbon components of other homologous series.

Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model

A recurring concern when studying biomolecules with molecular dynamics (MD) simulations is the accuracy of the underlying force field and solvent model. These considerations are especially relevant for simulations of intrinsically disordered peptides and proteins, for which energy differences between conformations are small and interactions with water are enhanced. In this work, we investigate the accuracy of the AMBER ff99SB force field, combined with either the TIP3P or the TIP4P-Ew water model, using both conventional MD and replica exchange MD (REMD) simulations to generate conformational ensembles for (disordered) trialanine, triglycine, and trivaline peptides.We find that the TIP4P-Ew water model yields significantly better agreement with experimentally measured scalar couplings - and therefore more accurate conformational ensembles - for both trialanine and triglycine. For trivaline, however, we find that the TIP3P and TIP4P-Ew ensembles are equivalent in accuracy. To address this discrepancy and further improve the force field, we derive new van der Waals parameters for alkanes in TIP4P-Ew water and a straightforward perturbation to the f backbone dihedral potential that shifts the β-PPII equilibrium. Of the two, we find that the revised f backbone dihedral potential is more effective and yields significantly improved conformational ensembles for both the trialanine and trivaline peptides in TIP4P-Ew water.

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.

Modeling VLE of H2+ Hydrocarbon Mixtures Using a Group Contribution SAFT with akijCorrelation Method Based on London’s Theory

A group contribution perturbed-chain statistical associating fluid theory (GC-PC-SAFT) equation of state (Tamouza et al. Fluid Phase Equilib. 2004, 222−223, 67−76) combined with a recent method for correlating kij using only pure compound parameters (NguyenHuynh et al. Ind. Eng. Chem. Res., 2008. 47(22), 8847−8858) is extended here to model vapor−liquid phase equilibria of H2 + alkanes and H2 + aromatics mixtures. The correlation of kij is inspired by London’s theory of dispersive interactions, and uses “pseudo-ionization energies” Ji and Jj of compounds i and j as adjustable parameters. The GC-PC-SAFT parameters for alkanes and aromatics were reused from previous works when available. Otherwise, the missing parameters were estimated by regression of corresponding pure vapor−liquid equilibrium (VLE) data. Those of H2 were determined in this work by correlating some VLE data of H2 + n-alkane systems. Using the parameters thus obtained, the phase envelopes of other H2 + alkane and H2 + aromatic systems were fully predicted. The prediction tests were as comprehensive as possible. Correlations and predictions are qualitatively and quantitatively satisfactory. The deviations are within 5−6%, that is, comparable to those obtained on previously investigated systems. Mixtures containing H2 are modeled here with deviations that compare well with those of the Grayson−Streed model (Grayson, H.G.; Streed, C.W.; Proc., 6th World Pet. Congress, 1963, 169−181), which is often used by process engineers for hydrogen and hydrocarbon mixtures.

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.

The Pleistocene vermicular red earth in South China signaling the global climatic change: The molecular fossil record

The trace molecular fossils identified in the Pleistocene vermicular red earth by using the gas chromatography-mass spectrometry (GC/MS) analysis include n -alkanes, n -alkanoic acids, n -alkanols and n -alkan-2-ones. The variations of the n -alkane parameters appear to bear significant climate information, in striking contrast to the oxygen-bearing molecules ( n -alkanoic acids and n -alkanols) believed to be more easily reworked by post-depositional processes. Of importance in paleoclimate reconstruction are the ratios of C 27 /C 31 n -alkane indicative of the replacement of woody plants by grassy vegetation, and C 15—21 /C 22—33 n -alkane representative of the relative abundance between microorganisms and higher plants. The profile trends of the two n -alkane ratios are comparable to the marine oxygen isotope record among stages 4—20. These molecular fossil records implicate that the Pleistocene vermicular red earth widespread in South China was formed in coupling to the global climatic change and could be an important climate carrier.

Gas‐phase and liquid‐state properties of esters, nitriles, and nitro compounds with the OPLS‐AA force field

AbstractNonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley &amp; Sons, Inc. J Comput Chem 22: 1340–1352, 2001

Solubility of gases in butanols

Abstract Solubilities of 15 nonpolar gases (He, Ne, Ar, Kr, Xe, H 2 , D 2 , N 2 , O 2 , CH 4 , C 2 H 4 , C 2 H 6 , CF 4 , SF 6 , and CO 2 ) in 2-methyl-2-propanol ( tert -butanol) have been measured at the temperature 303.15 K and 101.33 kPa partial pressure of gas. Standard changes of the Gibbs energy of solution have been also determined from experimental data. The Lennard–Jones 6,12 pair potential parameters have been estimated for that solvent using the Scaled Particle Theory (SPT) and these parameters have been compared with those corresponding to the other isomers of butanol. It can be concluded that the derived energy parameters provide a measurement of the association of the alkanol. A version of the UNIFAC model has been applied and the corresponding interaction parameters for alkanes and alkanols have been determined.

Combinedab initio/empirical approach for optimization of Lennard-Jones parameters

Obtaining accurate Lennard–Jones (L-J) parameters is a vital part of the optimization of empirical force fields due to their significant contribution to condensed-phase properties. We present a novel approach to optimize L-J parameters via the use of ab initio data on interactions between rare gas atoms and model compounds combined with the reproduction of experimental pure solvent properties. Relative values of ab initio minimum interaction energies and geometries between helium or neon and model compounds were used to optimize the relative magnitude of the L-J parameters. Absolute values of the L-J parameters were determined by reproducing experimental heats of vaporization and molecular volumes for pure solvents. Application of the approach was performed on methane, ethane, and propane. Free energies of aqueous solvation and butane pure solvent and aqueous solvation calculations were used to test the developed L-J parameters. The new alkane parameters are similar or improved as compared with current empirical force field parameters with respect to experimental pure solvent properties and free energies of aqueous solvation. Also included is a description of the internal portion of the force field. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 334–348, 1998

Calculation of pure compound saturated enthalpies and saturated volumes with the PRSV equation of state. Revised k1 parameters for alkanes

AbstractThe Stryjek‐Vera (1986a) modification of the Peng‐Robinson (1976) equation of state has been used to predict heats of vaporization, enthalpies of saturated phases and saturated volumes for pure compounds ranging in molecular complexity from diatomic gases to compounds showing polarity and association.Heats of vaporization at the normal boiling temperature are reproduced within 2% for the majority of the compounds tested. Similar results were obtained for the enthalpy of the saturated phases. Revised k1 parameters of the PRSV equation of state are reported for alkanes.An empirical correction has been developed for calculating saturated liquid volumes from the liquid volumes given by the PRSV equation of state. For the range of reduced temperatures from 0.5 to 0.99, deviations from experimental values are smaller than 4%. Saturated vapor volumes calculated from the PRSV equation of state were found to be satisfactory for most technical calculations.

Thermodynamic properties of binary mixtures containing aldehydes. III. Analysis of the excess enthalpies and excess Gibbs energies of n-alkanal + cyclohexane mixtures in terms of an extended quasichemical group contribution model (DISQUAC)

The data available in the literature for the excess enthalpies of ethanal, propanal, butanal, or pentanal + cyclohexane and for the liquid—vapour equilibria of propanal + cyclohexane are examined on the basis of DISQUAC, a very simple extension of the quasi-chemical group contribution theory applied in Parts I and II to correlate and predict excess enthalpies and excess Gibbs energies of n-alkanal + n-alkane mixtures. Using the same four alkyl group increments as in Part II, to account for intramolecular effects in the n-alkanals, and adjusted values for the Gibbs energy and enthalpy of interchange of the formyl(CHO)-cyclohexane contact, the model provides a fairly consistent description of the excess enthalpies as functions of composition and n-alkanal chain length. Molar excess Gibbs energies are estimated for several n-alkanal + cyclohexane mixtures. The (CHO)-cyclohexane interchange parameters are slightly larger than the (CHO)-normal alkane parameters. Ketones (CO group) and esters (COO group) behave similarly.