n-Heptane under pressure: structure and dynamics from molecular simulations

Atomistic molecular dynamics simulations have been performed in the isothermal-isobaric ensemble to explore the phase behavior of n-heptane. Motivated by recent high-pressure spectroscopic experiments on n-heptane, the present work aims at understanding the liquid-solid and the alluded to solid-solid transitions upon increasing pressure. Starting from the stabilized solid phase at 300 K and 10 kbar, we have investigated the range of these two transitions by a gradual decrease and increase of pressure, respectively. Although the solid-liquid transition has clear signatures such as the formation of gauche defects along the molecular backbone, the present model does not show any sign of a first-order solid-solid transition at high pressures. However, interesting changes in the environment around methyl groups and in their dynamics are observed. These have been substantiated by calculations of the vibrational density of states obtained from a normal-mode analysis and from the simulation trajectory.     

Comparison of the capillary wave method and pressure tensor route for calculation of interfacial tension in molecular dynamics simulations

We have studied the calculation of surface and interfacial tension for a variety of liquid–vapor and liquid–liquid interfaces using molecular dynamics (MD) simulations. Because of the inherently small scale of MD systems, large pressure fluctuations can cause imprecise calculations of surface tension using the pressure tensor route. The capillary wave method exhibited improved precision and stability throughout all of the simulated systems in this study. In order to implement this method, the interface was defined by fitting an error function to the density profile. However, full mapping of the interface from coordinate files produced enhanced accuracy. Upon increasing the system size, both methods exhibited higher precision, although the capillary wave method was still more reliable. © 2013 Wiley Periodicals, Inc.     

Determination of the polymer tacticity from calculation of infrared spectra based on classical molecular simulations

The infrared absorption spectra of poly(tetrafluoroethylene), PTFE, and poly(chlorotrifluoroethylene), PCTFE, are simulated using a method based on a combination of classical molecular simulations of the amorphous polymer phase with Kramers-Kronig relations. The differences and the analogies between experimental and calculated spectra of the non-stereoregular fluoride polymer, PTFE, are first reported. The isotactic and syndiotactic configurations of PCTFE are then investigated. The comparison between experimental and simulated spectra is established on a vibrational analysis. It reveals the preferred syndiotactic configuration adopted by the PCTFE chain.     

Extracting parameters for base-pair level models of DNA from molecular dynamics simulations

 A method is described to extract a complete set of sequence-dependent energy parameters for a rigid base-pair model of DNA from molecular dynamics (MD) simulations. The method is properly consistent with equilibrium statistical mechanics and leads to effective inertia parameters for the base-pair units as well as stacking and stiffness parameters for the base-pair junctions. We give explicit formulas that yield a complete set of base-pair model parameters in terms of equilibrium averages that can be estimated from a time series generated in an MD simulation. The expressions to be averaged depend strongly both on the choice of coordinates used to describe rigid-body orientations and on the choice of strain measures at each junction. Received: 12 July 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001     

Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations

The 1-octanol-water partition coefficient log K(ow) of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC∕E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K(ow) using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation.     

On the pressure calculation for polarizable models in computer simulation

We present a short overview of pressure calculation in molecular dynamics or Monte Carlo simulations. The emphasis is given to polarizable models in order to resolve the controversy caused by the paper of M. J. Louwerse and E. J. Baerends [Chem. Phys. Lett. 421, 138 (2006)] about pressure calculation in systems with periodic boundaries. We systematically derive expressions for the pressure and show that despite the lack of explicit pairwise additivity, the pressure formula for polarizable models is identical with that of nonpolarizable ones. However, a strict condition for using this formula is that the induced dipole should be in perfect mechanical equilibrium prior to pressure calculation. The perfect convergence of induced dipoles ensures conservation of energy as well. We demonstrate using more cumbersome but exact methods that the derived expressions for the polarizable model of water provide correct numerical results. We also show that the inaccuracy caused by imperfect convergence of the induced dipoles correlates with the inaccuracy of the calculated pressure.     

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods

Changes in the configurational entropies of molecules make important contributions to the free energies of reaction for processes such as protein-folding, noncovalent association, and conformational change. However, obtaining entropy from molecular simulations represents a long-standing computational challenge. Here, two recently introduced approaches, the nearest-neighbor (NN) method and the mutual-information expansion (MIE), are combined to furnish an efficient and accurate method of extracting the configurational entropy from a molecular simulation to a given order of correlations among the internal degrees of freedom. The resulting method takes advantage of the strengths of each approach. The NN method is entirely nonparametric (i.e., it makes no assumptions about the underlying probability distribution), its estimates are asymptotically unbiased and consistent, and it makes optimum use of a limited number of available data samples. The MIE, a systematic expansion of entropy in mutual information terms of increasing order, provides a well-characterized approximation for lowering the dimensionality of the numerical problem of calculating the entropy of a high-dimensional system. The combination of these two methods enables obtaining well-converged estimations of the configurational entropy that capture many-body correlations of higher order than is possible with the simple histogramming that was used in the MIE method originally. The combined method is tested here on two simple systems: an idealized system represented by an analytical distribution of six circular variables, where the full joint entropy and all the MIE terms are exactly known, and the R,S stereoisomer of tartaric acid, a molecule with seven internal-rotation degrees of freedom for which the full entropy of internal rotation has been already estimated by the NN method. For these two systems, all the expansion terms of the full MIE of the entropy are estimated by the NN method and, for comparison, the MIE approximations up to third order are also estimated by simple histogramming. The results indicate that the truncation of the MIE at the two-body level can be an accurate, computationally nondemanding approximation to the configurational entropy of anharmonic internal degrees of freedom. If needed, higher-order correlations can be estimated reliably by the NN method without excessive demands on the molecular-simulation sample size and computing time.     

Free volume from molecular dynamics simulations and its relationships to the positron annihilation lifetime spectroscopy

The free volume micro-structural properties of propylene glycol obtained by means of molecular dynamics simulations have been investigated and compared with the experimental data from positron annihilation lifetime spectroscopy (PALS). The results are also compared to those recently obtained on glycerol. The bulk microstructures of the samples have been analyzed in the temperature range 100–350 K with a probe-based procedure for exploring the free volume cavities of the microstructures. The basic free volume property, i.e., mean cavity volume, is compared with the hole volume data from PALS. A comparison between calculated and experimental data suggests the existence of a threshold volume for the smallest cavity detectable by PALS, which may be ascribed to fast local motions of the matrix constituents. At high temperatures the cavity analysis reveals the formation of an infinite cavity, i.e., percolation phenomenon. The onset temperatures of the percolation process in propylene glycol and glycerol are found to be close to the characteristic PALS temperature \(T^{\rm L}_{\rm b2}\) , where a pronounced change in the PALS response occurs, as well as to the characteristic dynamic Schönhals temperature \(T^{\rm SCH}_{\rm B}\) , and Stickel’s temperature \(T^{\rm ST}_{\rm B}\) , marking a dramatic change in the primary α properties.     

Empirical procedure for the calculation of ionization constants of organic compounds in water from their molecular volume

An empirical procedure was used to calculate 278 ionization constants of 271 organic compounds, including phenols, NH acids, benzoic acid derivatives, and mono- and dihydric carboxylic acids, in water. The examined compounds were divided into 11 structural groups. The ionization constants for compounds belonging to a single group were calculated from constant empirical coefficients, molecular volumes, and formulas with an average error of less than 3.5%, the maximal error not exceeding 9.9%.     

Dimer models for ErbB-2/neu transmembrane domains from molecular dynamics simulations

Interest in the transmembrane receptors tyrosine kinase of the erbB family is high due to the involvement of some of the members in human cancers. The original oncogenic alleles of neu discovered in rat neuroectodermal tumors lead to single Val664Glu substitution within the predicted transmembrane domain. Identical substitution at the homologous position 659 constitutively activates the oncogenic potential of the human ErbB-2 receptor by enhanced receptor dimer formation. The precise molecular details of receptor dimerization are still unknown and to acquire more knowledge of the mechanisms involved, molecular dynamics simulations are undertaken to study transmembrane dimer association. Transmembrane helices are predicted to associate in left-handed coiled-coil structures stabilized by Glu-Glu interhelix hydrogen bonds in the mutated form. The internal dynamics reveals π helix deformations which modify the helix-helix interface. Predicted models agree with those suggested from polarized IR and magic-angle spinning NMR spectroscopy. Received: 24 April 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998     

On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm

Widely used programs for molecular dynamics simulation of (bio)molecular systems are the Verlet and leapfrog algorithms. In these algorithms, the particle velocities are less accurately propagated than the positions. Important quantities for the simulation such as the temperature and the pressure involve the squared velocities at full time steps. Here, we derive an expression for the squared particle velocity at full time step in the leapfrog scheme, which is more accurate than the standardly used one. In particular, this allows us to show that the full time step kinetic energy of a particle is more accurately computed as the average of the kinetic energies at previous and following half steps than as the square of the average velocity as implemented in various molecular dynamics codes. Use of the square of the average velocity introduces a systematic bias in the calculation of the instantaneous temperature and pressure of a molecular dynamics system. We show the consequences when the system is coupled to a thermostat and a barostat.     

Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations

Through the use of the one-step perturbation approach, 130 free energies of base stacking and 1024 free energies of base pairing in DNA have been calculated from only five simulations of a nonphysical reference state. From analysis of a diverse set of 23 natural and unnatural bases, it appears that stacking free energies and stacking conformations play an important role in pairing of DNA nucleotides. On the one hand, favourable pairing free energies were found for bases that do not have the possibility to form canonical hydrogen bonds, while on the other hand, good hydrogen-bonding possibilities do not guarantee a favourable pairing free energy if the stacking of the bases dictates an unfavourable conformation. In this application, the one-step perturbation approach yields a wealth of both energetic and structural information at minimal computational cost.     

The use of two-phase molecular dynamics simulations to determine the phase behavior and critical point of propane molecular models

Molecular dynamics simulations were performed to determine two-phase configurations of model propane molecules below the critical point and in the near-critical, two-phase region. A postprocessor that uses a Monte Carlo method for determination of volumes attributable to each molecule was used to obtain density histograms of the particles from which the bulk coexisting equilibrium vapor and liquid densities were determined. This method of analyzing coexisting densities in a two-phase simulation is straightforward and can be easily implemented for complex, multisite models. Various degrees of internal flexibility in the propane models have little effect on the coexisting densities at temperatures 40 K or more below the critical point, but internal flexibility (angle bending and bond vibrations) does affect the saturated liquid densities in the near-critical region, changing the critical temperature by approximately 20 K. Shorter cutoffs were also found to affect the phase dome and the location of the critical point.     

A comparison of methods for melting point calculation using molecular dynamics simulations

Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed.     

Micellar crystals in solution from molecular dynamics simulations

Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.