Solution systems model aqueous solutions modeling

Semenova, M.G. (1996). Factors determining the character of biopolymer-biopolymer interactions in multicomponent aqueous solutions modelling food systems. In Parris, N., Kato, A., Creamer, L.K., Pearce, J. (Eds). Macromolecular Interactions in Food Technology, ACS Symposium Series No. 650, Washington, D.C. American Chemical Society, pp. 37 19. 

The simplest solution to increase the sampling of biomolecular systems is to perform longer simulations. Ten years ago, the time scale accessible for peptide simulation in explicit solvent was on the order of 100 ps [37, 38]. Today simulations of this length are routinely used in structural refinement and modelling studies. At present, about 1 s of CPU time on a fast processor is required to compute 1 fs of an MD trajectory of a small biomolecular system in aqueous solution with a total of 5000 atoms. This means that about one day on one processor is required to compute a 100 ps MD trajectory for such a system. However, about one year on 300 processors is required to compute a 1 is MD trajectory for such a system. Thus, the maximum accessible time scale is usually on the order of 100 ns for solvated biomolecules [39, 40]. 

Figure 1.2. Models of various parts comprising overall natural water systems (a) aqueous solution phase model (b) aqueous solution and gas phase model (c) aqueous solution and solid phase model (d) three-phase aqueous, gas, and solid phase model (e) aqueous solution plus several solid phases model and (f) multiphase model for solids, aqueous solution, and a gas phase.

In our next project we have investigated with much effort and in great detail the mechanochemical hydrolysis mechanism of the simplest disulfide model system in aqueous solution—substitution at sulfur. For the first time in a calculation, the enigmatic biphasic behavior of the reaction rate as a function of applied force obtained from force-clamp AFM experiments, see [13], has been reproduced in silico [24]... 

Most of what is known about the mechanisms leading to various types of DNA damages has been obtained by studying low-molecular-weight model systems. In aqueous solutions all the... 

Figure 12. Schematic state diagram of temperature vs. w% solute for an aqueous solution of a hypothetical small carbohydrate (representing a model frozen food system), illustrating the critical relationship between Tg and freezer temperature (Tf), and the resulting impact on the physical state of the freeze-concentrated amorphous matrix. (Reproduced with permission from reference 18. Copyri t 1988 Cambridge.)...

Combined NMR and MD has been successfully used by Widmalm coworkers to improve the models for carbohydrates and to gain detailed insight into structure and dynamics of these systems in aqueous solution. ... 

Due to its structure, the Achard model is a predictive model. Considering a mixed electrolyte solution (e.g. water-NaCl-KCl), it is possible to calculate the activities of all the species and constituents of the media, because the interaction parameters are from binary water-electrolyte systems. However, it is an aqueous solution model where water must always be included in the constituents of the system. 

Obviously, to model these effects simultaneously becomes a very complex task. Hence, most calculation methods treat the effects which are not directly related to the molecular structure as constant. As an important consequence, prediction models are valid only for the system under investigation. A model for the prediction of the acidity constant pfQ in aqueous solutions cannot be applied to the prediction of pKj values in DMSO solutions. Nevertheless, relationships between different systems might also be quantified. Here, Kamlet s concept of solvatochro-mism, which allows the prediction of solvent-dependent properties with respect to both solute and solvent [1], comes to mind. 

The aromatic shifts that are induced by 5.1c, 5.If and S.lg on the H-NMR spectrum of SDS, CTAB and Zn(DS)2 have been determined. Zn(DS)2 is used as a model system for Cu(DS)2, which is paramagnetic. The cjkcs and counterion binding for Cu(DS)2 and Zn(DS)2 are similar and it has been demonstrated in Chapter 2 that Zn(II) ions are also capable of coordinating to 5.1, albeit somewhat less efficiently than copper ions. Figure 5.7 shows the results of the shift measurements. For comparison purposes also the data for chalcone (5.4) have been added. This compound has almost no tendency to coordinate to transition-metal ions in aqueous solutions. From Figure 5.7 a number of conclusions can be drawn. (1) The shifts induced by 5.1c on the NMR signals of SDS and CTAB... 

The interactions between water and aqueous solutions and another phase have been modeled in various ways. The most simple models consist of an aqueous system in contact with a hard or soft wall described by... 

One femily of models for systems in non-aqueous solution are referred to as Self-Consistent Reaction Field (SCRF) methods. These methods all model the solvent as a continuum of uniform dielectric constant e the reaction field. The solute is placed into a cavity within the solvent. SCRF approachs differ in how they define the cavity and the reaction field. Several are illustrated below. 

A number of complexes of copper with 1,1-dithiolenes are known they are interesting, inasmuch as they form (1) polynuclear species, e.g., [Cu4(i-mnt)3]2 . Recently, a copper(III) complex of 1,1-dicarboeth-oxy-2-ethylenedithiolate (DED ) was prepared (375) by oxidation of aqueous solutions of K2[Cu(DED)2] with a 10-15% excess of Cu(II) or H202, and of (BzPh3P)2[Cu(DED)2] with I2. The possibility of this system as a model for the Cu "/Cu. system in n-galactose oxidase has been pointed out. Lewis and Miller (113) also prepared M[Cu(S2C CHN02)2] (M = Cu, or Zn) and Cu[Cu S2C C(CN)2 2], and found that they are effective insecticides. 

To prevent insolubility resulting from uncontrolled aggregation of extended strands, two adjacent parallel or antiparallel yS-peptide strands can be connected with an appropriate turn segment to form a hairpin. The / -hairpin motif is a functionally important secondary structural element in proteins which has also been used extensively to form stable and soluble a-peptide y9-sheet arrangements in model systems (for reviews, see [1, 4, 5] and references therein). The need for stable turns that can bring the peptide strands into a defined orientation is thus a prerequisite for hairpin formation. For example, type F or II" turns formed by D-Pro-Gly and Asn-Gly dipeptide sequences have been found to promote tight a-pep-tide hairpin folding in aqueous solution. Similarly, various connectors have been... 

L. B. Kier, C.-K. Cheng, and R Seybold, Cellular automata models of aqueous solution systems. Rev. Comput. Chem. 2001, 17, 205-254. 

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