Molecular dynamics simulations cation

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

For the 1,3-dithiane-1-oxide (R=H) case molecular dynamics simulations at the experimental temperature revealed that the R-hydroxysulfoniiun cation was considerably more stable than the more weakly adsorbed 1,3-dithiane molecule We consider that the hydroxydithiane cation may act as a proton transfer agent and this may account for the enhanced reactivity of this system. 

The CH cation 1, protonated methane, is the parent of hypercoordinated carbocations containing a five coordinated carbon atom. It is elusive in solution and has not been observed by NMR spectroscopy but gas-phase infrared investigations have shown its fluxional structure which has been proven by ab initio molecular dynamic simulation.18... 

An interesting combined use of discrete molecular and continuum techniques was demonstrated by Floris et al.181,182 They used the PCM to develop effective pair potentials and then applied these to molecular dynamics simulations of metal ion hydration. Another approach to such systems is to do an ab initio cluster calculation for the first hydration shell, which would typically involve four to eight water molecules, and then to depict the remainder of the solvent as a continuum. This was done by Sanchez Marcos et al. for a group of five cations 183 the continuum model was that developed by Rivail, Rinaldi et al.14,108-112 (Section III.2.ii). Their results are compared in Table 14 with those of Floris et al.,139 who used a similar procedure but PCM-based. In... 

Figure 2.9 Glucose-cation (solid line) and glucose-anion (dashed line) center-of-mass radial distribution functions calculated from molecular dynamics simulations of a single sugar molecule in [CjCjlm]Cl.

Kim and Klein96,100 have investigated SbF5 in liquid HF by ab initio molecular dynamics simulation. They observed the formation of Sbl fi ion and a very fast diffusion of the proton along the hydrogen-bonded HF chains. The cationic species is the protonated HF chain, in good agreement with experimental results.101... 

According to a recent ab initio molecular dynamic simulation study639 formation of formyl cation 328 is optimally favored in the 1 1 HF-SbF5 solution. No evidence, however, was found for the formation of the isoformyl cation 329 and diprotonated CO. The fast proton exchange observed earlier was suggested to occur between HCO+ and HF(HF) or SbF6. ... 

Anions bind also to other metals, like gold, platinum, or silver [74,81], Why do anions adsorb specifically to metals, while cations do not The explanation is a strong hydration of cations. A cation would have to give up its hydration shell for an adsorption. This is energetically disadvantageous. Anions are barely hydrated and can therefore bind more easily to metals [82], Another possible explanation is the stronger van der Waals force between anions and metals. The binding of ions to metallic surfaces is not yet understood and even the idea that cations are not directly bound to the metal, was questioned based on molecular-dynamics simulations [83],... 

Crown ethers continue to be one of the most useful parts of supramolecular chemistry/91 From the beginning computations of metal ions complexes with synthetic ionophores/101 which have been aptly reviewed/111 emphasized the importance of including explicitly solvation in free energy calculations, also with ab initio calculations on calixarene complexes/121 Molecular dynamics simulations of 18-crown-6 ether complexes in aqueous solutions predict too low affinities, but at least correctly reproduce the sequence trend K+ > Rb+ > Cs+ > Na+. However, only the selection of K+ over Rb+ and Cs+ is ascribed to the cation size relative to that of the crown cavity, whereas K+ appears in these calculations to be selected over Na+ as consequence of the greater free energy penalty involved in displacing water molecules ftomNa/1131... 

Wipff, G. (2001) Molecular dynamics simulations of cation complexation and extraction, in Vicens, J., Asfari, Z., Harrowfield, J., Bohmer, V. (eds.), Calixarenes-2001, Kluwer Acad. Publishers, Dordrecht, pp 312-333 and references cited therein. 

For the Tar—Tar kissing loops, the P—B calculations are unable to discern their propensity to accumulate counterions accumulation at the loop—loop interface (data not shown). This is because the fully hydrated ions as defined by the Stem layer cannot penetrate into the central cation binding pocket (data not shown). Similarly, the axial spine of counterion density observed in the A-RNA helix (Fig. 20.5) is not captured by the P—B calculation (Fig. 20.7). No noticeable sequence specificity is observed in the counterion accumulation patterns in the P—B calculations, even though the sequence effects are explicitly represented in the P—B calculation through the appropriate geometry and assignment of point-charges. This is because the sequence specificity observed in the molecular dynamics simulations usually involves first shell interactions of base moieties with partially dehydrated ions, which cannot be accurately represented in the P—B framework. 

Oelschlaeger P, Klahn M, Beard WA et al (2007) Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations improved accuracy in studies of structural features and mutational effects. J Mol Biol 366 687-701. doi 10.1016/J.Jmb. 2006.10.095... 

Based on the position of an ion in the Hoftneister series, it is possible to foretell the relative effectiveness of anions or cations in an enormous number of systems. The rank of an ion was related to its kosmotropicity, surface tension increments, and salting in and salting out of salt solutions (see below) [25]. A quantitative physical chemistry description of this phenomenon is not far off. Molecular dynamics simulations that considered ionic polarizability were found to be valuable tools for elucidating salt effects [26,27]. 

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