Lukas D. Schuler

An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase

Over the past 4 years the GROMOS96 force field has been successfully used in biomolecular simulations, for example in peptide folding studies and detailed protein investigations, but no applications to lipid systems have been published yet. Here we provide a detailed investigation of aliphatic liquid systems. For liquids of larger aliphatic chains, n‐heptane and longer, the standard GROMOS96 parameter sets 43A1 and 43A2 yield a too low pressure at the experimental density. Therefore, a reparametrization of the GROMOS96 force field regarding aliphatic carbons was initiated. The new force field parameter set 45A3 shows considerable improvements for n‐alkanes, cyclo‐, iso‐, and neoalkanes and other branched aliphatics. Liquid densities and heat of vaporization are reproduced for almost all of these molecules. Excellent agreement is found with experiment for the free energy of hydration for alkanes. The GROMOS96 45A3 parameter set should, therefore, be suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.

A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline Lα phase. Variants of the force-field parameter set as well as different sets of simulation conditions or simulation parameter sets are evaluated. In the case of the force-field parameters, the van der Waals constants for the non-bonded interaction of the ester carbonyl carbon and the partial charges and charge group definition of the phosphatidylcholine head group are examined. On the methodological side, different cut-off distances for the non-bonded interactions, use of a reaction-field force due to long-range electrostatic interactions, the frequency of removal of the centre of mass motion and the strength of the coupling of the pressure of the system to the pressure bath are tested. The area per lipid, as a measure of structure, the order parameters of the chain carbons, as a measure of membrane fluidity, and the translational diffusion of the lipids in the plane of the bilayer are calculated and compared with experimental values. An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed.

On the Choice of Dihedral Angle Potential Energy Functions for n-Alkanes

Abstract The parameters of the GROMOS96 force field governing dihedral angle transitions in aliphatic chains have been reconsidered, since these parameters produce a too large ratio of trans to gauche conformations in such chains. A refined set of parameters for dihedral angle interactions and third-neighbour interactions involving CH2 and CH3 atoms is proposed. They were obtained by fitting to the heat of vaporization, pressure and trans-gauche ratio for liquids of three n-alkanes, n-butane, n-pentane and n-hexane. The new parameter set does reproduce better these quantities and should therefore be more appropriate for use in simulations of polymers and membranes. A comparison of the mentioned properties obtained from simulations with united-atom models and from simulations with an all-atom model shows that the latter does not necessarily yield an improved description of molecular behaviour.

Molecular dynamics simulation of n -dodecyl phosphate aggregate structures

Abstract. Aggregates of n-dodecyl phosphate present an attractive model system of simple phospholipid amphiphile supramolecular structures for study by molecular dynamics simulation, since these systems have previously been studied experimentally under various conditions. A detailed molecular dynamics description of the properties of planar bilayer membranes (as a model for unilamellar vesicular membranes) and spherical micelles under various simulated conditions is presented. It is shown that the united-atom model of GROMOS96 applying the force-field parameter set 43A2 for biomolecular systems yields properties in agreement with experimental ones in most cases. Hydrogen bonding plays a role in stabilizing the bilayer aggregates at low pH, but not for the micelles, which are energetically favoured at high pH. NMR –SCD order parameters for a lipid bilayer system, the diffusion of amphiphiles within aggregates and of counterions, and lifetimes of hydrogen bonds between amphiphiles and to water are estimated from the MD simulations.

How Anionic Vesicles Steer the Oligomerization of Enzymatically Oxidized p-Aminodiphenylamine (PADPA) toward a Polyaniline Emeraldine Salt (PANI-ES)-Type Product

The oxidation of the aniline dimer, p-aminodiphenylamine (PADPA), with Trametes versicolor laccase and O2 in an aqueous solution of pH 3.5 is controlled by negatively charged AOT (sodium bis(2-ethylhexyl) sulfosuccinate) vesicles. With vesicles, a product resembling polyaniline in its emeraldine salt form (PANI-ES) is obtained, in contrast to the reaction without vesicles where no such product is formed. To understand this observation, the product distribution and structures from the reaction with and without vesicles were determined by using partially selectively deuterated PADPA as a starting material and analyzing the products with HPLC-MS. We found that in the presence of vesicles the main product is obtained in about 50% yield, which is the N-C-para-coupled PADPA dimer that has spectroscopic properties of PANI-ES, as determined by time-dependent density functional theory (TD-DFT) calculations. A secondary reaction route leads to longer PADPA oligomers that must contain a phenazine core. Without vesicles, PADPA and its products undergo partial hydrolysis, but in the presence of vesicles, hydrolysis does not occur. Because molecular dynamics (MD) simulations show that the main intermediate oxidation product is embedded within the vesicle membrane, where the water content is very low, we propose that the microenvironment of the vesicle membrane protects the oxidation products from unwanted hydrolysis.

Understanding the Enhanced Magnetic Response of Aminocholesterol Doped Lanthanide-Ion-Chelating Phospholipid Bicelles

Cholesterol (Chol-OH) and its conjugates are powerful molecules for engineering the physicochemical and magnetic properties of phospholipid bilayers in bicelles. Introduction of aminocholesterol (3β-amino-5-cholestene, Chol-NH2) in bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and the thulium-ion-chelating phospholipid 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA/Tm3+) results in unprecedented high magnetic alignments by selectively tuning the magnetic susceptibility Δχ of the bilayer. However, little is known on the underlying mechanisms behind the magnetic response and, more generally, on the physicochemical forces governing a Chol-NH2 doped DMPC bilayer. We tackled this shortcoming with a multiscale bottom-up comparative investigation of Chol-OH and Chol-NH2 mixed with DMPC. First, simplified monolayer models on a Langmuir trough were employed to compare the two steroid molecules at various contents in DMPC. In a second step, a molecular dynamics (MD) simulation allowed for a more representative model of the bicelle bilayer while monitoring the amphiphiles and their interactions on the molecular level. In a final step, we moved away from the models and investigated the effect of temperature on the structure and magnetic alignment of Chol-NH2 doped bicelles by SANS. The DMPC/steroid monolayer studies showed that Chol-OH induces a larger condensation effect than Chol-NH2 at steroid contents of 16 and 20 mol %. However, this tendency was inversed at steroid contents of 10, 30, and 40 mol %. Although the MD simulation with 16 mol % steroid revealed that both compounds induce a liquid-ordered state in DMPC, the bilayer containing Chol-NH2 was much less ordered than the analogous system containing Chol-OH. Chol-NH2 underwent significantly more hydrogen bonding interactions with neighboring DMPC lipids than Chol-OH. It seems that, by altering the dynamics of the hydrophilic environment of the bicelle, Chol-NH2 changes the crystal field and angle of the phospholipid-lanthanide DMPE-DTPA/Tm3+ complex. These parameters largely determine the magnetic susceptibility Δχ of the complex, explaining the SANS results, which show significant differences in magnetic alignment of the steroid doped bicelles. Highly magnetically alignable DMPC/Chol-NH2/DMPE-DTPA/Tm3+ (molar ratio 16:4:5:5) bicelles were achieved up to temperatures of 35 °C before a thermoreversible rearrangement into nonalignable vesicles occurred. The results confirm the potential of Chol-NH2 doped bicelles to act as building blocks for the development of the magnetically responsive soft materials of tomorrow.

How experimental details matter. The case of a laccase-catalysed oligomerisation reaction

The Trametes versicolor laccase (TvL)-catalysed oligomerisation of the aniline dimer p-aminodiphenylamine (PADPA) was investigated in an aqueous medium of pH = 3.5, containing 80–100 nm-sized anionic vesicles formed from AOT, the sodium salt of bis(2-ethylhexyl)sulfosuccinic acid. If run under optimal conditions, the reaction yields oligomeric products which resemble the emeraldine salt form of polyaniline (PANI-ES) in its polaron state, known to be the only oxidation state of linear PANI which is electrically conductive. The vesicles serve as “templates” for obtaining products with the desired PANI-ES-like features. For this complex, heterogeneous, vesicle-assisted, and enzyme-mediated reaction, in which dissolved dioxygen also takes part as a re-oxidant for TvL, small changes in the composition of the reaction mixture can have significant effects. Initial conditions may not only affect the kinetics of the reaction, but also the outcome, i.e., the product distribution once the reaction reaches its equilibrium state. While a change in the reaction temperature from T ≈ 25 to 5 °C mainly influenced the rate of reaction, increase in enzyme concentration and the presence of millimolar concentrations of chloride ions were found to have significant undesired effects on the outcome of the reaction. Chloride ions, which may originate from the preparation of the pH = 3.5 solution, inhibit TvL, such that higher TvL concentrations are required than without chloride to yield the same product distribution for the same reaction runtime as in the absence of chloride. With TvL concentrations much higher than the elaborated value, the products obtained clearly were different and over-oxidised. Thus, a change in the activity of the enzyme was found to have influence not only on kinetics but also led to a change in the final product distribution, molecular structure and electrical properties, which was a surprising find. The complementary analytical methods which we used in this work were in situ UV/vis/NIR, EPR, and Raman spectroscopy measurements, in combination with a detailed ex situ HPLC analysis and molecular dynamics simulations. With the results obtained, we would like to recall the often neglected or ignored fact that it is important to describe and pay attention to the experimental details, since this matters for being able to perform experiments in a reproducible way.