Nico F. A. van der Vegt

Validation of the 53A6 GROMOS force field

The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)2, and a proteinogenic β3-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding–unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.

What Is the Contact Angle of Water on Graphene

Although experimental and theoretical studies have addressed the question of the wetting properties of graphene, the actual value of the contact angle of water on an isolated graphene monolayer remains unknown. While recent experimental literature indicates that the contact angle of water on graphite is in the range 90-95°, it has been suggested that the contact angle on graphene may either be as high as 127° or moderately enhanced in comparison with graphite. With the support of classical molecular dynamics simulations using empirical force-fields, we develop an argumentation to show that the value of 127° is an unrealistic estimate and that a value of the order of 95-100° should be expected. Our study establishes a connection between the variation of the work of adhesion of water on graphene-based surfaces and the interaction potential between individual water molecules and these surfaces. We show that a variation of the contact angle from 90° on graphite to 127° on graphene would imply that both of the first two carbon layers of graphite contribute approximately the same interaction energy with water. Such a situation is incompatible with the short-range nature of the interaction between water and this substrate. We also show that the interaction potential energy between water and the graphene-based substrates is the main contribution to the work of adhesion of water with a relative magnitude that is independent of the number of graphene layers. We introduce the idea that the remaining contribution is entropic in nature and is connected to the fluctuations in the water-substrate interaction energy.

Cation specific binding with protein surface charges

Biological organization depends on a sensitive balance of noncovalent interactions, in particular also those involving interactions between ions. Ion-pairing is qualitatively described by the law of “matching water affinities.” This law predicts that cations and anions (with equal valence) form stable contact ion pairs if their sizes match. We show that this simple physical model fails to describe the interaction of cations with (molecular) anions of weak carboxylic acids, which are present on the surfaces of many intra- and extracellular proteins. We performed molecular simulations with quantitatively accurate models and observed that the order K+ < Na+ < Li+ of increasing binding affinity with carboxylate ions is caused by a stronger preference for forming weak solvent-shared ion pairs. The relative insignificance of contact pair interactions with protein surfaces indicates that thermodynamic stability and interactions between proteins in alkali salt solutions is governed by interactions mediated through hydration water molecules.

Systematic coarse-graining methods for soft matter simulations - a review

Multiscale modelling of soft matter is an emerging field that has made rapid progress in the past decade. Several methods for systematic coarse-graining of molecular liquids and soft matter systems have been proposed in recent years. Herein, we review these methods and discuss a selected number of applications as well as limitations of the models and remaining challenges in developing representative and transferable pair potentials.

Osmotic coefficients of atomistic NaCl (aq) force fields

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and four popular water models by means of effective ion-ion potentials. First we derive an effective potential at high dilution from simulations of two ions in explicit water. At higher ionic concentration multibody effects will become important. We propose to capture those by employing a concentration dependent dielectric permittivity. With the so obtained effective potentials we then perform implicit solvent simulations. We demonstrate that our effective potentials accurately reproduce ion-ion coordination numbers and the local structure. They allow us furthermore to calculate osmotic coefficients that can be directly compared with experimental data. We show that the osmotic coefficient is a sensitive and accurate measure for the effective ion-ion interactions and the intermediate-range structure of the solution. It is therefore a suitable and useful quantity for validating and parametrizing atomistic ion-water force fields.

Multiscale modeling of soft matter: scaling of dynamics

Many physical phenomena and properties of soft matter systems are characterized by an interplay of interactions and processes that span a wide range of length- and time scales. Computer simulation approaches require models, which cover these scales. These are typically multiscale models that combine and link different levels of resolution. In order to reach mesoscopic time- and length scales, necessary to access material properties, coarse-grained models are developed. They are based on microscopic, atomistic descriptions of systems and represent these systems on a coarser, mesoscopic level. While the connection between length scales can be established immediately, the link between the different time scales that takes into account the faster dynamics of the coarser system cannot be obtained directly. In this perspective paper we discuss methods that link the time scales in structure based multiscale models. Concepts which try to rigorously map dynamics of related models are limited to simple model systems, while the challenge in soft matter systems is the multitude of fluctuating energy barriers of comparable height. More pragmatic methods to match time scales are applied successfully to quantitatively understand and predict dynamics of one-component soft matter systems. However, there are still open questions. We point out that the link between the dynamics on different resolution levels can be affected by slight changes of the system, as for different tacticities. Furthermore, in two-component systems the dynamics of the host polymer and of additives are accelerated very differently.

Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate

Based on coarse grained simulations of a specially adapted model for bisphenol-A polycarbonate (BPA-PC) we generate by inverse mapping, the reintroduction of chemical details, well equilibrated all-atom conformations and time trajectories of dense polymeric melts for up to 7.8 µs. This is several orders of magnitude more than any direct all-atom simulations have reached so far. These polymer melts contain up to 68600 atoms in = 100 chains of molecular weight = 5217. By comparison with short all-atom simulations we show that these trajectories are physically meaningful, providing us with a powerful tool to compare long time simulations to experiments, which probe specific local dynamics on long time scales, such as NMR relaxation.

Free energy calculations of small molecules in dense amorphous polymers. Effect of the initial guess configuration in molecular dynamics studies

The excess free energy of small molecules in the amorphous polymers poly(ethylene) and poly(dimethylsiloxane) was calculated, using the test-particle-insertion method. The method was applied to polymer configurations obtained from molecular dynamics simulations with differently prepared initial guess configurations. It was found that the calculated solubility coefficients strongly depend on the quality of the initial guess configuration. Slow compression of dilute systems, during which process only the repulsive parts of the nonbonded Lennard-Jones potentials are taken into account, yields polymer melts which are better relaxed, and which offer lower solubilities for guest molecules compared with polymer melts generated at the experimental density or prepared by compressing boxes with soft-core nonbonded potentials. For the last two methods initial stresses relax by straining the internal modes (bond angles, torsion angles) of the chains

Hofmeister Ion Interactions with Model Amide Compounds

Dissolved electrolytes interact with peptides and proteins in aqueous solution. Herein, we study small amide compounds in aqueous electrolyte solutions and link their salting-in and salting-out propensities to molecular-level structural details obtained with molecular simulations. Aqueous solutions of NaF, NaCl, NaBr, NaI, NaNO(3), and NaClO(4) with N-isopropylacrylamide (NiPAM) and N-methylacetamide (NMA) have been investigated. Our results show that NiPAM is salted-in by NaI, mediated through iodide interactions with nonpolar groups, while being salted-out by the other salts. Hydrogen-bonding interactions of anions with the amide group of NiPAM could not be identified, while in the systems with NMA all Hofmeister anions formed stable hydrogen bonds with the amide group. These results indicate that the immediate chemical environment of the backbone amide groups should be considered in studies of protein destabilization by dissolved electrolytes. We furthermore report that all salts but NaI provoke a hydrophobic collapse transition of poly(N-isopropylacrylamide) in water at 300 K, in qualitative agreement with experimentally measured salt effects on the lower critical solution temperature of this system.

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation

We discuss the development of a coarse-grained (CG) model for molecular dynamics (MD) simulation of a hydrophobic dipeptide, diphenylalanine, in aqueous solution. The peptide backbone is described with two CG beads per amino acid, the side groups and charged end groups are each described with one CG bead. In the derivation of interaction functions between CG beads we follow a bottom-up strategy where we devise potentials such that the resulting CG simulation reproduces the conformational sampling and the intermolecular interactions observed in an atomistic simulation of the same peptide. In the CG model, conformational flexibility of the peptide is accounted for through a set of intra-molecular (bonded) potentials. The approach followed to obtain the bonded potentials is discussed in detail. The CG potentials for nonbonded interactions are based on potentials of mean force obtained by atomistic simulations in aqueous solution. Following this approach, solvent mediation effects are included in the effective bead-bead nonbonded interactions and computationally very efficient (solvent-free) simulations of self-assembly processes can be performed. We show that the conformational properties of the all-atom dipeptide in explicit solvent can be accurately reproduced with the CG model. Moreover, preliminary simulations of peptide self-assembly performed with the CG model illustrate good agreement with results obtained from all-atom, explicit solvent simulations.