Insights into Noncovalent Binding Obtained from Molecular Dynamics Simulations

Micellar Composition Affects Lipid Accretion Kinetics in Molecular Dynamics Simulations: Support for Lipid Network Reproduction

Mixed lipid micelles were proposed to facilitate life through their documented growth dynamics and catalytic properties. Our previous research predicted that micellar self-reproduction involves catalyzed accretion of lipid molecules by the residing lipids, leading to compositional homeostasis. Here, we employ atomistic Molecular Dynamics simulations, beginning with 54 lipid monomers, tracking an entire course of micellar accretion. This was done to examine the self-assembly of variegated lipid clusters, allowing us to measure entry and exit rates of monomeric lipids into pre-micelles with different compositions and sizes. We observe considerable rate-modifications that depend on the assembly composition and scrutinize the underlying mechanisms as well as the energy contributions. Lastly, we describe the measured potential for compositional homeostasis in our simulated mixed micelles. This affirms the basis for micellar self-reproduction, with implications for the study of the origin of life.

An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica

The effect of immobilized $$\upbeta$$ β -cyclodextrin (bCD) molecules inside a mesoporous silica support on the uptake of benzene and p-nitrophenol from aqueous solution was investigated using all-atom molecular dynamics (MD) simulations. The calculated adsorption isotherms are discussed with respect to the free energies of binding for a 1:1 complex of bCD and the aromatic guest molecule. The adsorption capacity of the bCD-containing material significantly exceeds the amount corresponding to a 1:1 binding scenario, in agreement with experimental observations. Beside the formation of 1:2 and, to a lesser extent, 1:3 host:guest complexes, also host–host interactions on the surface as well as more unspecific host–guest interactions govern the adsorption process. The demonstrated feasibility of classical all-atom MD simulations to calculate liquid phase adsorption isotherms paves the way to a molecular interpretation of experimental data that are too complex to be described by empirical models.

Density variations of TMAO solutions in the kilobar range: Experiments, PC-SAFT predictions, and molecular dynamics simulations

We present measurements, molecular dynamics (MD) simulations, and predictions using Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) of the density of aqueous solutions in a pressure range from 1 bar to 5000 bar, a pressure regime that is highly relevant for both biochemical applications and the fundamental understanding of solvation. The accurate determination of density data of pressurized solutions remains challenging. We determined relative density changes from the variations in X-ray absorption through the sample and developed a new water parameter set for PC-SAFT modeling that is appropriate for high pressure conditions in the kilobar regime. As a showcase, we studied trimethylamine N-oxide (TMAO) solutions and demonstrated that their compressibility decreases with the TMAO content. This result is linked to the stabilizing effect of TMAO on the local H-bond network of water. Experiments and calculations, which represent two independent methods, are in very good agreement and are in accordance with results of force field molecular dynamics simulations of the same systems.

Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme

A new method is proposed to calculate alchemical free-energy differences based on molecular dynamics (MD) simulations, called the conveyor belt thermodynamic integration (CBTI) scheme. As in thermodynamic integration (TI), K replicas of the system are simulated at different values of the alchemical coupling parameter λ. The number K is taken to be even, and the replicas are equally spaced on a forward-turn-backward-turn path, akin to a conveyor belt (CB) between the two physical end-states; and as in λ-dynamics (λD), the λ-values associated with the individual systems evolve in time along the simulation. However, they do so in a concerted fashion, determined by the evolution of a single dynamical variable Λ of period 2π controlling the advance of the entire CB. Thus, a change of Λ is always associated with K/2 equispaced replicas moving forward and K/2 equispaced replicas moving backward along λ. As a result, the effective free-energy profile of the replica system along Λ is periodic of period 2 πK^-1, and the magnitude of its variations decreases rapidly upon increasing K, at least as K^-1 in the limit of large K. When a sufficient number of replicas is used, these variations become small, which enables a complete and quasi-homogeneous coverage of the λ-range by the replica system, without application of any biasing potential. If desired, a memory-based biasing potential can still be added to further homogenize the sampling, the preoptimization of which is computationally inexpensive. The final free-energy profile along λ is calculated similarly to TI, by binning of the Hamiltonian λ-derivative as a function of λ considering all replicas simultaneously, followed by quadrature integration. The associated quadrature error can be kept very low owing to the continuous and quasi-homogeneous λ-sampling. The CBTI scheme can be viewed as a continuous/deterministic/dynamical analog of the Hamiltonian replica-exchange/permutation (HRE/HRP) schemes or as a correlated multiple-replica analog of the λD or λ-local elevation umbrella sampling (λ-LEUS) schemes. Compared to TI, it shares the advantage of the latter schemes in terms of enhanced orthogonal sampling, i.e. the availability of variable-λ paths to circumvent conformational barriers present at specific λ-values. Compared to HRE/HRP, it permits a deterministic and continuous sampling of the λ-range, is expected to be less sensitive to possible artifacts of the thermo- and barostating schemes, and bypasses the need to carefully preselect a λ-ladder and a swapping-attempt frequency. Compared to λ-LEUS, it eliminates (or drastically reduces) the dead time associated with the preoptimization of a biasing potential. The goal of this article is to provide the mathematical/physical formulation of the proposed CBTI scheme, along with an initial application of the method to the calculation of the hydration free energy of methanol.