Molecular Dynamics with Solvation

A very detailed description of solvent effects, along with temperature effects from nuclear motion (typically with classical nuclei), is obtained from average computed chiroptical response properties computed along the trajectory of a 

Glycine Change in Molar Rotation (A[4]) as a Function of Solvent-Solute Distance 

---

In order to determine what interactions dominate the optical rotation of methyloxirane in water, Mukhopadhayay et al. [151] have calculated the optical rotation of the solute-solvent system by including an explicit solvent shell in the calculations. Additional calculations were performed on the solvent shell alone, with the methyloxirane removed. Explicit solvent molecules were modeled by molecular dynamics. Implicit solvation was also considered, modeled by the COSMO continuum model. The optical rotation calculations were performed at the BP86/aug-cc-pVDZ level of theory and did not include zero-point vibrational... 

Elber, R. (1990). Calculation of the Potential of Mean Force Using Molecular Dynamics with Linear Constraints An Application to a Conformational Transition in a Solvated Peptide. I. Chem. Phvs. 93(6) 4312-4321. 

R. Elber, Calculation of the potential of mean force using molecular dynamics with linear constraints An application to a conformational transition in a solvated dipeptide. J. Chem. Phys. 93, 4312 (1990). 

Molecular dynamics with periodic boundary conditions is presently the most widely used approach for studying the equilibrium and dynamic properties of pure bulk solvent,97 as well as solvated systems. However, periodic boundary conditions have their limitations. They introduce errors in the time development of equilibrium properties for times greater than that required for a sound wave to traverse the central cell. This is because the periodicity of information flow across the boundaries interferes with the time development of other processes. The velocity of sound through water at a density of 1 g/cm3 and 300 K is 15 A/ps for a cubic cell with a dimension of 45 A, the cycle time is only 3 ps and the time development of all properties beyond this time may be affected. Also, conventional periodic boundary methods are of less use for studies of chemical reactions involving enzyme and substrate molecules because there is no means for such a system to relax back to thermal equilibrium. This is not the case when alternative ensembles of the constant-temperature variety are employed. However, in these models it is not clear that the somewhat arbitrary coupling to a constant temperature heat bath does not influence the rate of reequilibration from a thermally perturbed... 

For an understanding of protein-solvent interactions it is necessary to explore the modifications of the dynamics and structure of the surrounding water induced by the presence of the biopolymer. The theoretical methods best suited for this purpose are conventional molecular dynamics with periodic boundary conditions and stochastic boundary molecular dynamics techniques, both of which treat the solvent explicitly (Chapt. IV.B and C). We focus on the results of simulations concerned with the dynamics and structure of water in the vicinity of a protein both on a global level (i.e., averages over all solvation sites) and on a local level (i.e., the solvent dynamics and structure in the neighborhood of specific protein atoms). The methods of analysis are analogous to those commonly employed in the determination of the structure and dynamics of water around small solute molecules.163 In particular, we make use of the conditional protein solute -water radial distribution function,... 

Molecular Dynamics with Linear Constraints An Application to a Conformational Transition in a Solvated Dipeptide. 

Y. Sun andP. A. Kollman,/. Chem. Phys., 97,5108 (1992). Determination of Solvation Free Energy Using Molecular Dynamics with Solute Cartesian Mapping An Application to the Solvation of 18-Crown-6. 

Matrix columns (computing-related problem areas) software and interfaces (expert systems, development and maintenance and incentives) systems biology (chemistry, physics, and processes—complexity) molecular dynamics with quantitative reactive potentials chemical and physical environment of calculations (e.g., solvation) simulation-driven experiments special-purpose computing hardware closing the loop for computational chemistry with analytical instruments and methods database access, assessment, and traceability... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Often yon need to add solvent molecules to a solute before running a molecular dynamics simiilatmn (see also Solvation and Periodic Boundary Conditions" on page 62). In HyperChem, choose Periodic Box on the Setup m en ii to enclose a soln te in a periodic box filled appropriately with TIP3P models of water inole-cii les. 

The idea of a finite simulation model subsequently transferred into bulk solvent can be applied to a macromolecule, as shown in Figure 5a. The alchemical transformation is introduced with a molecular dynamics or Monte Carlo simulation for the macromolecule, which is solvated by a limited number of explicit water molecules and otherwise surrounded by vacuum. Then the finite model is transferred into a bulk solvent continuum... 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

This indicates that the polarity of a medium is a long-range property that goes much further than the first solvation shell and therefore involves the two adjacent bulk media properties. This result is, however, valid for compounds the solvation of which is not determined by specific interactions with the first solvent shell, but rather by long-range forces like dipole interactions. The solvation of DEPNA was determined by molecular dynamics too and similar conclusions were drawn [82]. 

---