Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization

Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

Getting the intermolecular forces correct: introducing the ASTA strategy for a water model

Having a force field for water providing good bulk properties is paramount for modern studies of most biological systems. Some of the most common three-site force fields are TIP3, SPC/ε or OPC3, providing a decent range of bulk properties. That does not mean though, that they have realistic inter-atomic forces. These force fields have been parameterized with a top-down approach, meaning, by fitting the force field parameters to the experimental bulk properties. This approach has been the governing strategy also for many variants of four- and more-site models. We test a bottom-up approach, in which the force field is parameterized by optimizing the non-bonded inter-atomic forces. Our philosophy is that correct inter-atomic forces lead to correct geometrical and dynamical properties. The first system we try to optimize with the accurately system tailored atomic (ASTA) approach is water, but we aim to eventually probe other systems in the future as well. We applied our ASTA strategy to find a good set of parameters providing accurate bulk properties for the simple three-site force field forms, and also for AMOEBA, a more detailed and polarizable force field. Even though our bottom-up approach did not provide satisfactory results for the simple three-site force fields (with fixed charges), for the case of the AMOEBA force field it led to a modification of the original strategy, giving very good intra- and inter-molecular forces, as compared to accurate quantum chemically calculated reference forces. At the same time, important bulk properties, in this study restricted to the density and diffusion, were accurately reproduced with respect to the experimental values.

Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases

The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25-30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, J. Am. Chem. Soc. 1992, 114, 7827-7843), a four-parameter Buckingham potential (Werhahn et al., Chem. Phys. Lett. 2015, 619, 133-138), or the three-parameter Morse potential (Morse, Phys. Rev. 1929, 34, 57-64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σij as ( 1 2 ( σ i 3 + σ j 3 ) ) 1 / 3 and one for the well-depth ϵij as ( 1 2 ( ϵ i - 2 + ϵ j - 2 ) ) - 1 / 2 . The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.

Diffusion of Water Molecules on the Surface of Silica Nanoparticles─Insights from Nuclear Magnetic Resonance Relaxometry

1H spin-lattice nuclear magnetic resonance (NMR) relaxation experiments have been performed for water dispersions of functionalized silica nanoparticles of diameters of 25 and 45 nm. The experiments have been performed in a broad frequency range spanning 3 orders of magnitude, from 10 kHz to 10 MHz, versus temperature, from 313 to 263 K. On the basis of the data, two-dimensional translation diffusion (diffusion close to the nanoparticle surface within a layer of the order of a few diameters of water molecules) has been revealed. The translational correlation times as well as the residence life times on the nanoparticle surface have been determined. It has turned out that the residence lifetime is temperature-independent and is on the order of 5 × 10-6 s for the smaller nanoparticles and by about a factor of 3 longer for the larger ones. The translational correlation time for the case of 25 nm nanoparticles is also temperature-independent and yields about 6 × 10-7 s, while for the dispersion of the larger nanoparticles, the correlation times changed from about 8 × 10-7 s at 313 K to about 1.2 × 10-6 s at 263 K. In addition to the quantitative characterization of the two-dimensional translation diffusion, correlation times associated with bound water molecules have been determined. The studies have also given insights into the population of the bound and diffusing water on the surface water fractions.

A transferable double exponential potential for condensed phase simulations of small molecules

The Lennard-Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present Smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy Smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard-Jones based force fields.