The Solvent Box

In Langevin dynamics studies, the solvent is simulated no solvent molecules are included explicitly in the calculation. The beauty of such calculations is their consequent speed. 

In Chapter 2, I mentioned that there was great interest in water as a solvent, and explained about the pioneering calculations of Rahman and Stillinger (1972). Many molecular mechanics (MM), Monte Carlo (MC) and molecular dynamics (MD) studies have been made based on their box of 216 water molecules. A good starting point is the work of Jorgensen and coworkers. 

Comparison of Simple Potential Functions for Simulating Liquid Water William L. Jorgensen, Jayaraman Chandresekhar and Jeffrey D. Madura Journal of Physical Chemistry 79 (1983) 926 

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The simulations in the dry and in the humid RTIL started with 12 crowns (Q form) "diluted" in the solvent box. The crowns rapidly underwent a conformational change to D3d, showing that this structure is more stable in the two forms of the RTIL. Typical snapshots at the end of the dynamics (1.5 ns) and radial distribution functions (see Figure 10) reveal the importance of solvent cations. 

The problems already mentioned at the solvent/vacuum boundary, which always exists regardless of the size of the box of water molecules, led to the definition of so-called periodic boundaries. They can be compared with the unit cell definition of a crystalline system. The unit cell also forms an "endless system without boundaries" when repeated in the three directions of space. Unfortunately, when simulating hquids the situation is not as simple as for a regular crystal, because molecules can diffuse and are in principle able to leave the unit cell. 

However, it is common practice to sample an isothermal isobaric ensemble NPT, constant pressure and constant temperature), which normally reflects standard laboratory conditions well. Similarly to temperature control, the system is coupled to an external bath with the desired target pressure Pq. By rescaling the dimensions of the periodic box and the atomic coordinates by the factor // at each integration step At according to Eq. (46), the volume of the box and the forces of the solvent molecules acting on the box walls are adjusted. 

HyperChem uses th e ril 31 water m odel for solvation. You can place th e solute in a box of T1P3P water m oleeules an d impose periodic boun dary eon dition s. You may then turn off the boundary conditions for specific geometry optimi/.aiion or molecular dynamics calculations. However, th is produces undesirable edge effects at the solvent-vacuum interface. 

CAUTION. Sodium must be handled with great care and under no circumstances may the metal be allowed to come into contact with water as a dangerous explosion may result. Sodium is stored under solvent naphtha or xylene it should not be handled with the fingers but with tongs or pincers. Waste or scrap pieces of sodium should be placed in a bottle provided for the purpose and containing solvent naphtha or xylene they should never be thrown into the sink or into the waste box. If it is desired to destroy the scrap sodium, it should be added in small portions to rather a large quantity of methylated spirit. 

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. 

HyperChem allows solvation of arbitrary solutes (including no solute) in water, to simulate aqueous systems. HyperChem uses only rectangular boxes and applies periodic boundary conditions to the central box to simulate a constant-density large system. The solvent water molecules come from a pre-equilibrated box of water. The solute is properly immersed and aligned in the box and then water molecules closer than some prescribed distance are omitted. You can also put a group of non-aqueous molecules into a periodic box. 

The electrolyte used is 1 molar LiPF dissolved in a mixture of 30% ethyl carbonate (EC) and 70% diethyl carbonate (DEC) by volume. This electrolyte IS easy to use because it will self-wet the separator and eleetrodes at atmospheric pressure. The electrolyte is kept under an argon atmosphere in the glove-box. The moleeules of electrolyte solvents, like EC and DEC, have in-plane dimensions of about (4 A x 5 A) to (6 A x 7 A). These molecules are normally larger than the openings of the micropores formed in the region 3 carbons (Fig. 2) as described in section 5. 

The idea is to embed the molecule of interest in a solvent box as shown in Figure 15.1 (aspirin in water). After this MM, MD or MC calculations can be made. A periodic box should be added as needed. 

A realistic model of a solution requires at least several hundred solvent molecules. To prevent the outer solvent molecules from boiling off into space, and minimizing surface effects, periodic boundary conditions are normally employed. The solvent molecules are placed in a suitable box, often (but not necessarily) having a cubic geometry (it has been shown that simulation results using any of the five types of space filling polyhedra are equivalent ). This box is then duplicated in all directions, i.e. the central box is suiTounded by 26 identical cubes, which again is surrounded by 98 boxes etc. If a... 

In a 70 ml culture tube equipped with a Teflon lined cap, 10 ml 0.2 M 7 was mixed with 10 ml 1 M Me3Al in CH2C12 solvent at 22 °C in a dry box under nitrogen atmosphere. After one hour the Me3Al was destroyed by slowly adding methanol to the mixture. The tube was withdrawn from the dry box, and the reaction mixture was washed with ice-cold 0.5 N HC1 solution and water, separated, dried over anhydrous MgS04, solvent was evaporated under vacuum, and the products were analyzed by H1 NMR spectroscopy. 

Our Box on page 799 explores the effects of equilibria on CO2 in the atmosphere, and Example shows that the acidity of the solvent places an upper limit on the amount of salt that will dissolve. 

The purity of recovered compounds depends on the pmity of all materials used in the PLC process, such as the solvents, and the cleanliness of the tank, sample containers, etc. Plates stored in cardboard boxes or plates with polymer binders exposed to light and air will become contaminated. Prewashing of plates by development with the mobile phase, methanol-dichloromethane (1 1), or 1% acetic acid or 1 % ammonium hydroxide in diethyl ether (depending on whether the subsequent mobile phase is acidic or basic) will clean the layer. The prewashed plates are vacuum-dried and stored in a vacuum desiccator prior to use to keep them clean. 

The fiuid-phase simulation approach with the longest tradition is the simulation of large numbers of the molecules in boxes with artificial periodic boundary conditions. Since quantum chemical calculations typically are unable to treat systems of the required size, the interactions of the molecules have to be represented by classical force fields as a prerequisite for such simulations. Such force fields have analytical expressions for all forces and energies, which depend on the distances, partial charges and types of atoms. Due to the overwhelming importance of the solvent water, an enormous amount of research effort has been spent in the development of good force field representations for water. Many of these water representations have additional interaction sites on the bonds, because the representation by atom-centered charges turned out to be insufficient. Unfortunately it is impossible to spend comparable parameterization work for every other solvent and... 

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