Rigid Force Fields Research Articles

Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: a systematic study of several common force fields.

We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

Vapor–liquid equilibria of ethylene (C2H4) + decafluorobutane (C4F10) at 268–298 K from experiment, molecular simulation and the Peng–Robinson equation of state

Isothermal vapor–liquid equilibrium (VLE) data are presented for the system ethylene+decafluorobutane. Measurements are performed for four isotherms around the critical temperature of ethylene, i.e. in the temperature range from 268.13 to 298.13K. The measurements are undertaken using a “static-analytic” type apparatus, sampling the phases in equilibrium via a moving capillary sampler (ROLSITM). The uncertainties of the present measurements of temperature, pressure and mole fraction are within 0.036K, 0.0058MPa and 0.02mol/mol, respectively. The VLE data are correlated with the Peng–Robinson equation of state (PR EOS), incorporating the Mathias–Copeman alpha function. Both, the Wong–Sandler mixing rule with the non-random two-liquid (NRTL) activity coefficient model and the quadratic Van der Waals one-fluid mixing rule are used. In addition, a new rigid force field model for decafluorobutane is developed and molecular simulations are carried out. The simulation results are compared to the present experimental data for the binary system. Furthermore, pure component properties of decafluorobutane are predicted and compared to experimental data from the literature and the PR EOS.

Flexible or rigid molecular models? A study on vapour–liquid equilibrium properties of ammonia

The influence of the intramolecular degrees of freedom on the vapour–liquid equilibrium properties of ammonia is studied for vapour pressure, saturated densities and enthalpy of vaporization. Molecular force fields with and without intramolecular degrees of freedom, keeping all other parameters unchanged, show significantly different phase envelopes. For ammonia, the angle potential is particularly important, because the hydrogen sites are more aligned in the liquid than in the vapour, leading to a significantly enhanced molecular dipole moment in the condensed phase. Based on a rigid force field for ammonia from prior work of our group [Eckl et al., Mol. Phys. 106, 1039 (2008)], a new accurate force field with intramolecular degrees of freedom is developed.

The quest for the best nonpolarizable water model from the adaptive force matching method

The recently introduced adaptive force matching (AFM) method is used to develop a significantly improved pair-wise nonpolarizable potential for water. A rigid version of the potential is also presented to enable larger time steps for biological simulations. In this work, it is demonstrated that the AFM method can be used to systematically assess the importance of each functional term during the construction of a force field. For a water potential, it is established that a single off-atom charge center (M) in the plane of water outperforms two out-of-plane charge sites for reproducing intermolecular forces. The four-site pair-wise nonpolarizable force field developed in this work rivals some of the most sophisticated polarizable models in terms of reproducing accurate ab initio forces. The force fields are parameterized to perform best in the temperature range from 0 to 40°C. Equilibrium and dynamical properties calculated with the flexible and rigid force fields are in good agreement with experimental results. For the flexible model, the agreement improves when path integral simulation is performed. These force fields provide high-quality results at a very low computational cost and are thus well suited to atomistic scale biological simulations. The AFM method provides a mechanism for selecting important terms in force field expressions and is a very promising tool for producing accurate force fields in condensed phases.

Force Field Validation for Molecular Dynamics Simulations of IRMOF-1 and Other Isoreticular Zinc Carboxylate Coordination Polymers

Molecular dynamics simulations were conducted to validate a hybrid force field for metal−organic framework-5 (IRMOF-1). In this force field, only nonbonded parameters are used to describe Zn−O interactions. The CVFF force field was used with slight modifications to describe the benzene dicarboxylate linker. The force field correctly predicts a wide range of structural properties of this MOF, including a negative thermal expansion of approximately 1% at 30 and 293 K, in agreement with both theory and experiment. Compressibility results and the associated elastic moduli are in also good agreement with published density functional theory calculations and nanoindentation experiments. The force field predicts a decrease in elastic moduli as temperature increases, which would greatly affect the mechanical properties of MOFs. Calculated vibrational frequencies for Zn−O modes agree with experiment, and a low-frequency mode representing a 180° rotation of the phenyl groups is seen. This rotation becomes more prevalent as the temperature is increased from 300 to 400 K, in agreement with NMR data. Simulations were also carried out with adsorbed guests, including ethanol, cyclohexane, and several chloromethanes. It is shown that the IRMOF-1 lattice parameter depends on the nature of the guest−framework interaction; strongly hydrophilic guests, such as ethanol, cause a decrease (−0.9%) in unit cell volume, while hydrophobic guests cause an increase (0.7−1.5%) in unit cell volume. The calculated free volumes in IRMOF-1 range from 53.5% to 56.0%, in good agreement with experiment. Finally, the activation energy for benzene self-diffusion calculated at low loadings is in good agreement with previous simulations and NMR results, but the magnitude of the diffusion constant is underestimated, most likely because of deficiencies in the CVFF portion of the force field. The results demonstrate, however, that employing a rigid force field results in much poorer agreement with experimental data. Additionally, a flexible force field approach is required when simulating framework stability because of physical changes or the presence of adsorbates. The use of a general-purpose force field for the organic components allows our approach to be extended to other Zn-based frameworks.

Energetics of Ion Permeation, Rejection, Binding, and Block in Gramicidin A from Free Energy Simulations

The rigid force fields currently used in molecular dynamics (MD) simulations of biomolecules are optimized for globular proteins. Whether they can also be used in MD simulations of membrane proteins is an important issue that needs to be resolved. Here we address this issue using the gramicidin A channel, which provides an ideal test case because of the simplicity of its structure and the availability of a wealth of functional data. Permeation properties of gramicidin A can be summarized as “it conducts monovalent cations, rejects anions, and binds divalent cations.” Hence, a comprehensive test should consider the energetics of permeation for all three types of ions. To that end, we construct the potential of mean force for K +, Cl −, and Ca 2+ ions along the channel axis. For an independent check of the potential-of-mean-force results, we also calculate the free energy differences for these ions at the channel center and binding sites relative to bulk. We find that “rejection of anions” is satisfied but there are difficulties in accommodating the other two properties using the current MD force fields.

Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure–function relations to force fields

Molecular dynamics simulations of membrane proteins have become a popular tool for studying their dynamic features, which are not easily accessible by experiments. Whether the force fields developed for globular proteins are adequate this purpose is an important question that is often glossed over. Here we determine the permeation properties of potassium ions in the gramicidin A channel in a lipid bilayer from free energy simulations, and compare the results to experimental data. In particular, we check the dependence of the free energy barriers ions face at the channel center on the membrane size. The results indicate that there is a serious problem with the current rigid force fields independent of the membrane size, and new, possibly polarizable, force fields need to be developed to resolve this problem.

Systematic molecular dynamics studies of liquid N,N-dimethylformamide using optimized rigid force fields: Investigation of the thermodynamic, structural, transport and dynamic properties

The properties of the pure liquid N,N-dimethylformamide were investigated by means of microcanonical (NVE) and isothermal–isobaric (NPT) molecular dynamics simulation techniques. Previously proposed five- and six-interaction-site optimized potential models (OPLS) were employed to simulate the liquid at different state points and their properties were obtained and discussed. The results obtained have shown that these models, to a higher or lower degree, yield realistic descriptions of the liquid. We have found, however, that a systematic readjustment of the potential parameters is necessary in order to describe the liquid properties more accurately. Thus, a new six-interaction-site OPLS computational model for liquid N,N-dimethylformamide has been derived. It turns out that this model can describe not only the thermodynamic and structural properties but also the dynamic (single and Debye relaxation) and the transport properties (self-diffusion, shear viscosity) of the system with good accuracy in the entire temperature range at normal pressure.