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Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations. [ABSTRACT FROM AUTHOR]

First-principles calculations within the density functional theory (DFT) framework have been performed in order to investigate various conformations of the 2,5-pyridine di-carboxylic acid (PDCA) molecule adsorbed onto the Cu(011) surface. By means of DFT calculations the adsorption geometry, the bond formation and the electronic properties of PDCA molecule conformations on the Cu(011) surface have been studied. The most important structural property is the orientation of the COOH H atom which can point either toward the aromatic ring or toward the vacuum. This H atom position determines the possible reactions in which the adsorbed molecule can get involved and also has a significant impact on the value of the Cu-molecule system work function. Thus, we find that simply by changing the H atom orientation (from up to down) the Cu-molecule system work function can be varied with more than 2.5 eV. This is a significant result as a lot of effort is put nowadays in finding efficient ways for the in situ variation of the systems work function. Scanning tunneling microscopy (STM) images, reflexion absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties (adsorption entropies, enthalpies) have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies (STM or RAIRS experiments). [ABSTRACT FROM AUTHOR]

A novel algorithm for modeling the influence of the host lattice flexibility in molecular dynamics simulations is extended to chain-like molecules and mixtures. This technique, based on a Lowe-Andersen thermostat, maintains the advantages of both simplicity and efficiency. The same diffusivities and other properties of the flexible framework system are reproduced. Advantageously, the computationally demanding flexible host lattice simulations can be avoided. Using this methodology we study the influence of flexibility on diffusion of n-alkanes inside single-walled carbon nanotubes. Furthermore, results are shown for diffusion of two mixtures (methane-helium and ethane-butane). Using these results we investigate the accuracy of theories describing diffusion in the Knudsen regime. For the dynamics in carbon nanotubes the Knudsen diffusivities are much too low. The Smoluchowski model gives better results. Interestingly, the extended Smoluchowski model can reproduce our simulation results obtained with a rigid host lattice. We modify this model to also treat collisions with a flexible interface correctly. As the tangential momentum accommodation coefficient is needed for the theoretical models, we introduce a simple concept to calculate it. [ABSTRACT FROM AUTHOR]

In order to efficiently calculate chemical equilibria of large molecules in a confined environment the reactive Monte Carlo technique is combined with the configurational-bias Monte Carlo approach. To prove that detailed balance is fulfilled the acceptance rule for this combination of particular Monte Carlo techniques is derived in detail. Notably, by using this derivation all other acceptance rules of any Monte Carlo trial moves usually carried out in combination with the configurational-bias Monte Carlo approach can be deduced from it. As an application of the combination of reactive and configurational-bias Monte Carlo the influence of different zeolitic confinements (MFI, TON, LTL, and FER) on the reaction equilibrium and the selectivity of the propene metathesis reaction system was investigated. Compared to the bulk phase the conversion is increased significantly. The authors study this reaction system in the temperature range between 300 and 600 K, and the pressure range from 1 to 7 bars. In contrast to the bulk phase, pressure and temperature have a strong influence on the composition of the reaction mixture in confinement. At low pressures and temperatures both conversion and selectivity are highest. Furthermore, the equilibrium composition is strongly dependent on the type of zeolite. This demonstrates the important role of the host structure in catalytic systems. [ABSTRACT FROM AUTHOR]

We describe a novel algorithm that includes the effect of host lattice flexibility into molecular dynamics simulations that use rigid lattices. It uses a Lowe-Andersen thermostat for interface-fluid collisions to take the most important aspects of flexibility into account. The same diffusivities and other properties of the flexible framework system are reproduced at a small fraction of the computational cost of an explicit simulation. We study the influence of flexibility on the self-diffusion of simple gases inside single walled carbon nanotubes. Results are shown for different guest molecules (methane, helium, and sulfur hexafluoride), temperatures, and types of carbon nanotubes. We show, surprisingly, that at low loadings flexibility is always relevant. Notably, it has a crucial influence on the diffusive dynamics of the guest molecules. [ABSTRACT FROM AUTHOR]