Hamaker Constants for Bionano Interactions in Water

Physical Chemistry Chemical Physics, 2019

We discuss an application of a density functional approach to describe a bilayer, or a simplified model of a membrane, that is built of tethered chain molecules. The bilayer integrity is maintained by tethering chain particles to two common sheets. We study the structure of a two-component mixture in contact with the bilayer, as well as the solvation force acting between two bilayers, immersed in a fluid. The fluid is a binary mixture involving the component that can cross freely the bilayer and the second impenetrable component. All the calculations are carried out for athermal system, in which only hard-core interactions are present.

We present a method of modeling nanoparticle (NP) hydrophobicity using coarse-grained molecular dynamics (CG MD) simulations, and apply this to the interaction of lipids with nanoparticles. To model at a coarse-grained level the wettability or hydrophobicity of a given material, we choose the MARTINI coarse-grained force field, and determine through simulation the contact angles of MARTINI water droplets residing on flat regular surfaces composed of various MARTINI bead types (C1, C2, etc.). Each surface is composed of a single bead type in each of three crystallographic symmetries (FCC, BCC, and HCP). While this method lumps together several atoms (for example, one cerium and two oxygens of CeO 2) into a single CG bead, we can still capture the overall hydrophobicity of the actual material by choosing the MARTINI bead type that gives the best fit of the contact angle to that of the actual material, as determined by either experimental or all-atom simulations. For different MARTINI bead types, the macroscopic contact angle is obtained by extrapolating the microscopic contact angles of droplets of eight different sizes (containing N w = 3224−22978 water molecules) to infinite droplet size. For each droplet, the contact angle was computed from a best fit of a circular curve to the droplet interface extrapolated to the first layer of the surface. We then examine how small nanoparticles of differing wettability interact with MARTINI dipalmitoylphosphotidylcholine (DPPC) lipids and SP-C peptides (a component of lung surfactant). The DPPC shows a transition from tails coating the nanoparticle to a hemimicelle coating the water-wet NP, as the contact angle of a water droplet on the surface is lowered below ∼60°. The results are relevant to developing a taxonomy describing the potential nanotoxicity of nanoparticle interactions with components in the lung.

Nature Materials, 2009

The Journal of Chemical Physics, 2009

We investigate the solvent mediated interactions between nanoparticles adsorbed at a liquidvapor interface in comparison to the solvent mediated interactions in the bulk liquid and vapor phases of a Lennard-Jones solvent. Molecular dynamics simulation data for the latter are in good agreement with results from integral equations in the reference functional approximation and a simple geometric approximation. Simulation results for the solvent mediated interactions at the interface differ markedly from the interactions of the particles in the corresponding bulk phases.

The work presents the detailed analysis of the water dimer properties. Their parameters are investigated on the basis of a multipole interaction potential extended up to the quadrupole--quadrupole and dipole--octupole terms. All main equilibrium parameters of the dimer are obtained: its geometry, ground-state energy, dipole and quadrupole moments, vibration frequencies, {\it etc}. They are thoroughly compared with those obtained in quantum chemical calculations and from spectroscopic data. The efficiency of the present model potentials is discussed. A new viewpoint on the nature of the hydrogen bond is presented. The results of studies are thoroughly compared with the spectroscopic and computer simulation data.

Nanoscopic Approaches in Earth and Planetary Sciences, 2010

nanoscale phenomena dominate many of the important processes near the surface of the earth. therefore these phenomena are of special importance to the environment and human health. as nanoscale processes are intrinsically molecular, there is an immediate synergy between the study of nanoscale particles in natural systems and the disciplines of mineralogy, chemistry, physics and materials science.

Physical Chemistry Chemical Physics, 2021

We present a multiscale computational approach for the first-principles study of bio-nano interactions. Using titanium dioxide as a case study, we evaluate the affinity of titania nanoparticles to water and biomolecules through atomistic and coarse-grained techniques.

The Journal of Physical Chemistry B, 2003

The purpose of this study was to determine the potentials of mean force (PMF) of the interactions between models of like-charged and between models of charged and nonpolar amino acid side chains in water to design improved side chain-side chain interaction potentials for our united residue UNRES force field for protein-structure prediction. Restrained molecular dynamics with the AMBER force field, the TIP3P model of water, and the Ewald summation were used to carry out simulations, and the weighted histogram analysis method (WHAM) was used to calculate the PMFs as functions of solute-solute distances. The following types of systems were considered to model the interactions between like-charged side chains and the interactions between charged and nonpolar side chains: (i) a pair of positively charged ions (potassium, ammonium, and guanidine, respectively); (ii) a pair of negatively charged ions (chloride and acetate, respectively), and (iii) pairs of methane with potassium, ammonium, and chloride ions, respectively. Additionally, a pair of potassium and chloride ions was included for comparison with the work of other authors. Except for the pair of acetate ions, where the PMF curve exhibited all-repulsive behavior, a minimum or two coalescing minima with positive PMF values appeared for pairs of like-charged ions. In the potassium-chloride ion pair, a contact and a solvent-separated minimum was observed. Comparison of our results with those obtained by other authors showed that including Ewald summation in computing electrostatic interactions has substantial influence on the PMFs of like-charged ions; for oppositely charged ions including Ewald summation only causes deepening of the contact minimum. It was found that the appearance of the minimum in the PMFs of likecharged ion pairs is caused by a high degree of ordering of water molecules and counterions between the solutes at this distance. The solvent contribution to the PMFs of pairs of charged and nonpolar solutes is positive in all cases; the most unfavorable contribution was observed for the methane-chloride ion pair. The results demonstrate that the use of all-repulsive potentials for the interactions between like-charged and between charged and nonpolar side chains in the UNRES force field is essentially correct, but the distance dependence should be more long range in the like-charged side chain interaction potential, because the PMF curves of like-charged ion pairs are reasonably fitted with a combination of r -1 , r -2 , and r -3 terms (r being the distance between the centers of the mass), while they are not reproduced well with combinations of r -6 and r -12 terms of the present version of UNRES.

Journal of Physical Chemistry B, 2008

The potentials of mean force of 21 heterodimers of the molecules modeling hydrophobic amino acid side chains: ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), methyl propyl sulfide (for methionine), and indole (for tryptophane) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay-Berne term to represent effective van der Waals interactions and the cavity term proposed in our earlier work were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, are well represented by the analytical expressions for all systems; large deviations between the MD-determined PMF and the analytical approximations are observed for pairs involving the least spheroidal solutes: ethylbenzene, indole, and methyl propyl sulfide at short distances at which the PMF is high and, consequently, these regions are rarely visited. When data from the PMF within only 10 kcal/mol above the global minimum are considered, the standard deviation between the MD-determined and the fitted PMF is from 0.25 to 0.55 kcal/mol (the relative standard deviation being from 4% to 8%); it is larger for pairs involving nonspherical solute molecules. The free energies of contact computed from the PMF surfaces are well correlated with those determined from proteincrystal data with a slope close to that relating the free energies of transfer of amino acids (from water to n-octanol) to the average contact free energies determined from protein-crystal data. These observations justify future use of the determined potentials in coarse-grained protein-folding simulations.

Semiconductor Physics Quantum Electronics and Optoelectronics

A new mechanism of interaction between two nanoparticles characterized by their dimensions and shape has been proposed. The mechanism is based on the local-field induced dipole momentum interaction with taking into account nonlinear polarizabilities of the particles. The dipole momentum induced in the particles has a fluctuating nature. The proposed mechanism of interparticle interaction leads to formation of both repulsive and attractive parts having the minimum at the distance between the particles close to their linear dimensions. The profile and strength of the potential depend both on dimensions and shapes of the particles as well as on their mutual orientation. Implementation of the discussed interaction conception to biology and medicine has been discussed.