Study of caffeine-DNA interaction in aqueous solution by parallel Monte Carlo simulation

Monte Carlo simulation of caffeine aqueous solutions containing a superhelical B-DNA fragment is performed using parallel computing. The binding sites of caffeine molecules with DNA were identified as well as the most probable structures of the resultant complexes. The degrees of caffeine molecule association in aqueous solutions with different concentrations were estimated and the main configuration types of molecular aggregates were revealed.     

The generalized van der Waals partition function. III. Local composition models for a mixture of equal size square-well molecules

New local composition models for mixtures of equal size molecules with differing attractive forces are presented, and compared with our results of Monte Carlo computer simulations for mixtures of square-well molecules which are also reported here. Unlike most previous local composition models, these new models predict random mixing in the high density limit and Boltzmann factor nonrandomness at low density; both limiting behaviors are in agreement with statistical mechanical theory. The predictions of these new models as a function of composition, density and temperature are in good agreement with the Monte Carlo computer simulation results.     

Combining reactive and configurational-bias Monte Carlo: confinement influence on the propene metathesis reaction system in various zeolites

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.     

Theoretical and numerical study of the phase diagram of patchy colloids: ordered and disordered patch arrangements

We report theoretical and numerical evaluations of the phase diagram for a model of patchy particles. Specifically, we study hard spheres whose surface is decorated by a small number f of identical sites ("sticky spots") interacting via a short-ranged square-well attraction. We theoretically evaluate, solving the Wertheim theory, the location of the critical point and the gas-liquid coexistence line for several values of f and compare them to the results of Gibbs and grand canonical Monte Carlo simulations. We study both ordered and disordered arrangements of the sites on the hard-sphere surface and confirm that patchiness has a strong effect on the phase diagram: the gas-liquid coexistence region in the temperature-density plane is significantly reduced as f decreases. We also theoretically evaluate the locus of specific heat maxima and the percolation line.     

Isodesmic self-assembly in lyotropic chromonic systems

We have developed simple models of chromonic molecules and by carrying out Monte Carlo simulation in a binary mixture of model chromonic and water molecules, have studied the effect of concentration and molecular shape on the pattern of molecular aggregation. We have also computed the free energy change associated with the formation of chromonic columnar aggregates by umbrella sampling. This helps us to verify the isodesmic behaviour which is characteristic of chromonic systems.     

Isodesmic self-assembly in lyotropic chromonic systems

We have developed simple models of chromonic molecules and by carrying out Monte Carlo simulation in a binary mixture of model chromonic and water molecules, have studied the effect of concentration and molecular shape on the pattern of molecular aggregation. We have also computed the free energy change associated with the formation of chromonic columnar aggregates by umbrella sampling. This helps us to verify the isodesmic behaviour which is characteristic of chromonic systems.     

Microscopic structure and solvation in dry and wet octanol

Octanol-water partition coefficients are extraordinarily successful for correlating and predicting numerous processes of pharmacological and environmental importance. The amphiphilic nature of the 1-octanol molecules allows the octanol phase to mimic the complexities of many different environments ranging from biomembranes to soil. However, the structural details of the octanol phase and whether its structure is altered upon water saturation are not yet fully understood. Configurational-bias Monte Carlo simulations in the Gibbs ensemble demonstrate that a diverse spectrum of hydrogen-bonded aggregates exists in dry and wet 1-octanol, and that water saturation substantially alters the 1-octanol environment from predominantly linear aggregates in dry octanol to larger cylindrical micelles with water cores in wet octanol. These simulation results are able to reconcile the conflicting views (chain-like or water-centered aggregates vs spherical micelles) of the 1-octanol structure inferred from thermodynamic arguments, spectroscopic measurements, and diffraction experiments. Calculated partition constants quantify the influence of water saturation on the solubility characteristics of the dry and wet octanol phases.     

Relation between pressure shift and electric-field shift of single-molecule lines in a polymer glass

The pressure shifts and the electric-field shifts of individual chromophores in an amporphous matrix are--due to strong disorder--subject to broad distributions. By means of single-molecule spectroscopy we measured both the pressure and the electric-field shift of about 800 tetra-tert-butylterrylene molecules in polyisobutylene. We found a significant correlation of 0.52 (Kendall's correlation coefficient) between the two observables. Analytical calculations and Monte Carlo simulations based on a model by Laird and Skinner predict a nonzero, yet, distinctly smaller correlation. The Monte Carlo simulations showed that the usual assumptions of a spherical shape and isotropic polarizability of the chromophores in glassy systems is an oversimplification of the complex nanoscopic structure and cannot reproduce our experimental results. By taking the molecular anisotropy into account, we obtain agreement of the simulated and the measured correlation between pressure shift and electric-field shift parameter.     

Modeling adsorption in metal-organic frameworks with open metal sites: propane/propylene separations

We present a new approach for modeling adsorption in metal-organic frameworks (MOFs) with unsaturated metal centers and apply it to the challenging propane/propylene separation in copper(II) benzene-1,3,5-tricarboxylate (CuBTC). We obtain information about the specific interactions between olefins and the open metal sites of the MOF using quantum mechanical density functional theory. A proper consideration of all the relevant contributions to the adsorption energy enables us to extract the component that is due to specific attractive interactions between the π-orbitals of the alkene and the coordinatively unsaturated metal. This component is fitted using a combination of a Morse potential and a power law function and is then included into classical grand canonical Monte Carlo simulations of adsorption. Using this modified potential model, together with a standard Lennard-Jones model, we are able to predict the adsorption of not only propane (where no specific interactions are present), but also of propylene (where specific interactions are dominant). Binary adsorption isotherms for this mixture are in reasonable agreement with ideal adsorbed solution theory predictions. We compare our approach with previous attempts to predict adsorption in MOFs with open metal sites and suggest possible future routes for improving our model.     

Computer simulation studies of aggregates of associating polymers: Influence of low-molecular-weight additives solubilizing the aggregates

The structure of aggregates in solutions of chain molecules with associating groups at one of the ends is studied by Monte Carlo computer simulations using the bond fluctuation model. The main attention is paid to the influence of additives of low-molecular-weight solvent solubilizing the aggregates. It is shown that upon the addition of solvent the aggregates adopt a three-layer structure with the ‘lake’ of the solvent molecules in the central region surrounded by the layer of associating end-groups of polymer chains, which in turn is surrounded by the outer corona formed by the chain tails. The equilibrium form of the aggregates becomes close to that of a droplet of low-molecular-weight liquids. The regimes are found when the addition of the low-molecular-weight solvent stabilizes the multiplets and even induces the aggregate formation.     

Adsorption of short heteropolymers in slitlike pores

Adsorption of short linear heteropolymers in slitlike pores is studied using the density functional theory and Monte Carlo simulations. The molecules are assumed to be freely jointed tangent hard spheres. The segments have different affinity with regard to the walls. Each molecule contains one surface-binding segment that interacts with the walls via Lennard-Jones (3,9) potential and a number of segments interacting with surfaces via the hard-wall potentials. A position of the surface-binding segment in the chain can be arbitrarily chosen. We have studied the influence of the pore width, the chain length and the chemical structure of molecules on adsorption and the microscopic structure of the confined fluid. The theoretical predictions are compared with Monte Carlo simulations carried out for different 'isomeric' pentamers.     

Biomolecule-directed assembly of nanoscale building blocks studied via lattice Monte Carlo simulation

We perform lattice Monte Carlo simulations to study the self-assembly of functionalized inorganic nanoscale building blocks using recognitive biomolecule linkers. We develop a minimal coarse-grained lattice model for the nanoscale building block (NBB) and the recognitive linkers. Using this model, we explore the influence of the size ratio of linker length to NBB diameter on the assembly process and the structural properties of the resulting aggregates, including the spatial distribution of NBBs and aggregate topology. We find the constant-kernel Smoluchowski theory of diffusion-limited cluster-cluster aggregation describes the aggregation kinetics for certain size ratios.     

Density functional approach to the adsorption of spherical molecules on a surface modified with attached short chains

A density functional and Monte Carlo simulation study of end-grafted polymers immersed by simple fluids is presented. The polymer molecules are modeled as freely jointed tangent hard spheres with the end segments linked to the surface. The authors analyze an influence of the chain length, the grafting density, and a nature of solvent on the brush structure. Adsorption of hard-sphere mixtures on the modified surface is also discussed. The theory precisely approximates simulation data.     

Kinetics of gold nanoparticle aggregation: experiments and modeling

We investigate the aggregation kinetics of gold nanoparticles using both experimental techniques (i.e., quasi-elastic light scattering, UV-visible spectroscopy, and transmission electron microscopy) and mathematical modeling (i.e., constant-number Monte Carlo). Aggregation of gold nanoparticles is induced by replacing the surface citrate groups with benzyl mercaptan. We show that the experimental results can be well described by the model in which interparticle interactions are described by the classical DLVO theory. We find that final gold nanoparticle aggregates have a fractal structure with a mass fractal dimension of 2.1-2.2. Aggregation of approximately 11 initial gold nanoparticles appears to be responsible for the initial color change of suspension. This kinetic study can be used to predict the time required for the initial color change of a gold nanoparticle suspension and should provide insights into the design and optimization of colorimetric sensors that utilize aggregation of gold nanoparticles.     

A perturbation density functional theory for the competition between inter and intramolecular association

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient.     

Grand canonical Monte Carlo simulation of the adsorption isotherms of water molecules on model soot particles

The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. The soot particles are modeled by graphite-type layers arranged in an onionlike structure that contains randomly distributed hydrophilic sites, such as OH and COOH groups. The calculated water adsorption isotherm at 298 K exhibits different characteristic shapes depending both on the type and the location of the hydrophilic sites and also on the size of the pores inside the soot particle. The different shapes of the adsorption isotherms result from different ways of water aggregation in or/and around the soot particle. The present results show the very weak influence of the OH sites on the water adsorption process when compared to the COOH sites. The results of these simulations can help in interpreting the experimental isotherms of water adsorbed on aircraft soot.     

Direct correlation functions of binary mixtures of hard Gaussian overlap molecules

We study the direct correlation function (DCF) of a classical fluid mixture of nonspherical molecules. The components of the mixture are two types of hard ellipsoidal molecules with different elongations, interacting through the hard Gaussian overlap (HGO) model. Two different approaches are used to calculate the DCFs of this fluid, and the results are compared. Here, the Pynn approximation [J. Chem. Phys. 60, 4579 (1974)] is extended to calculate the DCF of the binary mixtures of HGO molecules, then we use a formalism based on the weighted density functional theory introduced by Chamoux and Perera [J. Chem. Phys. 104, 1493 (1996)]. These results are fairly in agreement with each other. The pressure of this system is also calculated using the Fourier zero components of the DCF. The results are in agreement with the Monte Carlo molecular simulation.     

Chemical speciation of adsorbed glycine on metal surfaces

Experimental studies have reported that glycine is adsorbed on the Cu(110) and Cu(100) surfaces in its deprotonated form at room temperature, but in its zwitterionic form on Pd(111) and Pt(111). In contrast, recent density functional theory (DFT) calculations indicated that the deprotonated molecules are thermodynamically favored on Cu(110), Cu(100), and Pd(111). To explore the source of this disagreement, we have tested three possible hypotheses. Using DFT calculations, we first show that the kinetic barrier for the deprotonation reaction of glycine on Pd(111) is larger than on Cu(110) or Cu(100). We then report that the presence of excess hydrogen would have little influence on the experimentally observed results, especially for Pd(111). Lastly, we perform Monte Carlo simulations to demonstrate that the aggregates of zwitterionic species on Pt(111) are energetically preferred to those of neutral species. Our results strongly suggest that the formation of aggregates with relatively large numbers of adsorbed molecules is favored under experimentally relevant conditions and that the adsorbate-adsorbate interactions in these aggregates stabilize the zwitterionic species.     

Benchmarking the thermodynamic analysis of water molecules around a model beta sheet

Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P‐2005 and TIP5P‐Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the water–water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application. © 2012 Wiley Periodicals, Inc.