Vacuum molecular dynamics simulation

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Figure 1. History of the dihedral angle C3-C4-C5-05 calculated from a typical molecular dynamics simulation of a a-D-glucopyranose in the conformation in vacuum. (Reproduced from Ref. 9. Copyright 1986 American Chemical Society.)...

Molecular dynamics simulations on artificial surface-mounted molecular rotors have been performed and extensively reviewed.33 55 The theoretical rotational motion, driven by a circularly polarized electric field, of a dipolar chiral rhenium complex rotor attached to a molecular grid was also studied.56 In vacuum and at... 

Xia B, Tsui V, Case DA, Dyson J, Wright PE (2002) Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water, J Biomol NMR, 22 317-331... 

Although it is important to minimize the number of molecules in either Monte Carlo or molecular dynamics simulations for computational convenience, surface effects at the interface between the simulated solvent and the surrounding vacuum could seriously distort... 

NMR spectroscopy is a very useful tool for determining the local chemical surroundings of various atoms. Komin et al studied theoretically this for the adenine molecule of Fig. 20 both in vacuum and in an aqueous solution using different computational approaches. In all cases, density-functional calculations were used for the adenine molecule, but as basis functions they used either a set of localized functions (marked loc in Table 45) or plane waves (marked pw). Furthermore, in order to include the effects of the solvent they used either the polarizable continuum approach (marked PCM) or an explicit QM/MM model with a force field for the solvent and a molecular-dynamics approach for optimizing the structure (marked MD). In that case, the chemical shifts were calculated as averages over 40 snapshots from the molecular-dynamics simulations. Finally, in one case, an extra external potential from the solvent acting on the solute was included, too, marked by the asterisk in the table. 

A. Kohlmayer, W. Witschel, E. Spohr, Molecular dynamics simulation of water/metal and water/vacuum interfaces with a polarizable water model, Chem. Phys., 213 (1996) 211-216. 

Schmidt, R. K., Teo, B. and Brady, J. W. (1995). Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamics simulations. J. Phys. Chem., 99, 11339-11343. 

One major complication that distinguishes electrocatalytic reactions from catalytic reactions at metal-gas or metal-vacuum interfaces is the influence of the solvent. Modeling the role of the solvent in electrode reactions essentially started with the pioneering work of Marcus [68]. Originally these theories were formulated to describe relatively simple electron-transfer reactions, but more recently also ion-transfer reactions and bond-breaking reactions have been incorporated [69-71]. Moreover, extensive molecular dynamics simulations have been carried out to obtain a more molecular picture of the role of the solvent in charge-transfer processes, either in solution or at metal-solution interfaces. 

To explore these effects more thoroughly, results are presented from stochastic boundary molecular dynamics simulations of the active-site cleft of lysozyme in the presence of aqueous solvent and in vacuum.108 The simulation... 

The correlation function, <-P2[am(0) ( )]>. provides a measure of the internal motions of particular residues in the protein.324 333 Figure 46 shows the results obtained for Trp-62 and Trp-63 from the stochastic boundary molecular dynamics simulations of lysozyme used to analyze the displacement and velocity autocorrelation functions. The net influence of the solvent for both Trp-62 and Trp-63 is to cause a slower decay in the anisotropy than occurs in vacuum. In vacuum, the anisotropy decays to a plateau value of 0.36 to 0.37 (relative to the initial value of 0.4) for both residues within a picosecond. In solution there is an initial rapid decay, corresponding to that found in vacuum, followed by a slower decay (without reaching a plateau value) that continues beyond the period (10 ps) over which the correlation function is ex-... 

A. Kohlmeyer, W. Witschel, and E. Spohr Chem. Phys., 213, 211 (1997). Molecular Dynamics Simulations of Water/Metal and Water/Vacuum Interfaces with a Polarizable Water Model. 

Conformation and the Collective Motions of Protein Normal Mode Analysis and Molecular Dynamics Simulations of Melittin in Water and in Vacuum. 

Fig. 20.6 Snapshots from molecular dynamics simulations showing the evolution of nanopaiticles exposed to high O contents, water, and acid molecules. Top row shows pure Pt particles and bottom row displays Pt/PtCo/PtaCo particles (a) under vacuum, (b) under 0.5 ML of O and 0.5 ML of water, (c) under 0.6 ML of O and 0.6 ML of water, (d) under 0.75 ML of O and 0.75 ML of water, and (e) under 0.85 ML of O and 0.85 ML of water. In all cases acid molecules were added to the systems in an amount equivalent to have a pH of 3 (adapted from [120])...

Several molecular dynamics simulations have addressed this issue [14,74, 75], however the simplest model of a water wire consists of an hydrogen-bonded chain of water molecules in vacuum, constrained in space by harmonic poten-... 

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