Aqueous ion-containing interfaces are ubiquitous and play a key role in a plethora of physical, chemical, atmospheric, and biological processes, from which we mention just a few illustrative examples: (i) Ions at the air/water interface are important for atmospheric chemistry involving ocean surfaces and seawater aerosols, 1-5 as well as that of the Arctic snowpack covered by sea spray. 6,7 (ii) Many salts (such as NaCl) tend to inhibit bubble coalescence, 8-12 which is one of the reasons why foam is formed when waves break in the ocean but not in freshwater lakes. (iii) Brine rejection occurring at the seawater/ice interface has profound climatic effects in polar regions. 13 (iv) The aqueous electrolyte/metal interface is involved in electrode and corrosion processes. 14,15

Specific ion effects at the air/water interface.

We propose a modification in the three-dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab geometry that are periodic in two dimensions and have a finite length in the third dimension. The proposed method adds a correction term to the standard Ewald summation formula. To test the current method, molecular dynamics simulations on water between Pt(111) walls have been carried out. For a more direct test, the calculation of the pair forces between two point charges has been also performed. An excellent agreement with the results from simulations using the rigorous two dimensional Ewald summation technique were obtained. We observed that a significant reduction in computing time can be achieved when the proposed modification is used.

Ewald summation for systems with slab geometry

Until recently, “room-temperature” (<100–150 °C) liquid-state electrochemistry was mostly electrochemistry of diluted electrolytes(1)–(4) where dissolved salt ions were surrounded by a considerable amount of solvent molecules. Highly concentrated liquid electrolytes were mostly considered in the narrow (albeit important) niche of high-temperature electrochemistry of molten inorganic salts(5-9) and in the even narrower niche of “first-generation” room temperature ionic liquids, RTILs (such as chloro-aluminates and alkylammonium nitrates).(10-14) The situation has changed dramatically in the 2000s after the discovery of new moisture- and temperature-stable RTILs.(15, 16) These days, the “later generation” RTILs attracted wide attention within the electrochemical community.(17-31) Indeed, RTILs, as a class of compounds, possess a unique combination of properties (high charge density, electrochemical stability, low/negligible volatility, tunable polarity, etc.) that make them very attractive substances from fundamental and application points of view.(32-38) Most importantly, they can mix with each other in “cocktails” of one’s choice to acquire the desired properties (e.g., wider temperature range of the liquid phase(39, 40)) and can serve as almost “universal” solvents.(37, 41, 42) It is worth noting here one of the advantages of RTILs as compared to their high-temperature molten salt (HTMS)(43) “sister-systems”.(44) In RTILs the dissolved molecules are not imbedded in a harsh high temperature environment which could be destructive for many classes of fragile (organic) molecules.

/pdf/ionic-liquids-at-electrified-interfaces-4n93eaytys.pdf

Ionic Liquids at Electrified Interfaces

The term molecular mechanics (MM) refers to the use of simple potential-energy functions (e.g., harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, and ligand-docking simulations.

Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds. Internal forces experienced in the model structure are described using simple mathematical functions. For example, Hooke’s law is commonly used to describe bonded interactions, and the nonbonded atoms might be treated as inelastic hard spheres or may interact according to a Lennard-Jones potential. Using these simple models, a molecular dynamics simulation numerically solves Newton’s equations of motion, thus allowing structural fluctuations to be observed with respect to time.

Dynamic simulation methods are widely used to obtain information on the time evolution of conformations of proteins and other biological macromolecules1–4 and also kinetic and thermodynamic information. Simulations can provide fine detail concerning the motions of individual particles as a function of time. They can be utilized to quantify the properties of a system at a precision and on a time scale that is otherwise inaccessible, and simulation is, therefore, a valuable tool in extending our understanding of model systems. Theoretical consideration of a system additionally allows one to investigate the specific contributions to a property through “computational alchemy”,5 that is, modifying the simulation in a way that is nonphysical but nonetheless allows a model’s characteristics to be probed. One particular example is the artificial conversion of the energy function from that representing one system to that of another during a simulation. This is an important technique in free-energy calculations.6 Thus, molecular dynamics simulations, along with a range of complementary computational approaches, have become valuable tools for investigating the basis of protein structure and function.

This review offers an outline of the origin of molecular dynamics simulation for protein systems and how it has developed into a robust and trusted tool. This review then covers more recent advances in theory and an illustrative selection of practical studies in which it played a central role. The range of studies in which MD has played a considerable or pivotal role is immense, and this review cannot do justice to them; MD simulations of biomedical importance were recently reviewed.4 Particular emphasis will be placed on the study of dynamic aspects of protein recognition, an area where molecular dynamics has scope to provide broad and far-ranging insights. This review concludes with a brief discussion of the future potential offered to advancement of the biological and biochemical sciences and the remaining issues that must be overcome to allow the full extent of this potential to be realized.

1.1. Historical Background
MD methods were originally conceived within the theoretical physics community during the 1950s. In 1957, Alder and Wainwright7 performed the earliest MD simulation using the so-called hard-sphere model, in which the atoms interacted only through perfect collisions. Rahman8 subsequently applied a smooth, continuous potential to mimic real atomic interactions. During the 1970s, as computers became more widespread, MD simulations were developed for more complex systems, culminating in 1976 with the first simulation of a protein9,10 using an empirical energy function constructed using physics-based first-principles assumptions. MD simulations are now widely and routinely applied and especially popular in the fields of materials science11,12 and biophysics.

As will be discussed later in this review, a variety of experimental conditions may be simulated with modern theories and algorithms. The initial simulations only considered single molecules in vacuo. Over time, more realistic or at least biologically relevant simulations could be performed. This trend is continuing today.

The initial protein MD simulation, of the small bovine pancreatic trypsin inhibitor (BPTI), covered only 9.2 ps of simulation time. Modern simulations routinely have so-called equilibration periods much longer than that, and production simulations of tens of nanoseconds are routine, with the first microsecond MD simulation being reported in 1998.13 In addition, the original BPTI simulation included only about 500 atoms rather than the 104-106 atoms that are common today. While much of this advancement results from an immense increase in availability of computing power, major theoretical and methodological developments also contribute significantly.

The number of publications regarding MD theory and application of MD to biological systems is growing at an extraordinary pace. A single review cannot do justice to the recent applications of MD. Using data from ISI Web of Science, the authors estimate that during 2005 at least 800 articles will be published that discuss molecular dynamics and proteins. The historical counts are shown in Figure 1.






Open in a separate window


Figure 1


Articles matching ISI Web of Science query “TS=(protein) AND TS=(molecular dynamics)”.

/pdf/molecular-dynamics-survey-of-methods-for-simulating-the-45fcz5gua9.pdf

Molecular dynamics: survey of methods for simulating the activity of proteins.

We present results from theoretical studies of aqueous ionic solvation of alkali halides aimed at developing a microscopic description of structure and dynamics at the interface between air and sal...

Ions at the Air/Water Interface

Molecular dynamics computer simulations have been carried out for water enclosed between Pt(111) surfaces at high external electric fields. The dielectric constant of water as a function of electric fields has been calculated. Two-dimensional Ewald summation technique has been used for the calculation of long-range Coulombic forces. Simulations with a larger distance between walls, different surfaces, and bulk water have been done to confirm the macroscopic nature of the dielectric constant. Calculated dielectric constants have been compared with those obtained by a theoretical prediction and a recent simulation study.

Dielectric constant of water at high electric fields: Molecular dynamics study

Photodetachment spectra of Cl−(H2O)n clusters. Predictions and comparisons

Aqueous solution near charged Ag(111) surfaces: Comparison between a computer simulation and experiment

To understand how the inclusion of explicit polarizability into water interaction potential changes the structure of water next to a charged metallic surface we compared the results from the simulations using polarizable point charge model and simple point charge model To study the effect of density constraints we also performed simulations of water next to hydrophobic walls and metal walls In these simulations the water density was not predetermined, but regulated itself during the run

In Chul Yeh

Papers

Ewald summation for systems with slab geometry

Dielectric constant of water at high electric fields: Molecular dynamics study

Photodetachment spectra of Cl−(H2O)n clusters. Predictions and comparisons

Aqueous solution near charged Ag(111) surfaces: Comparison between a computer simulation and experiment

Effects of the polarizability and water density constraint on the structure of water near charged surfaces: Molecular dynamics simulations