The molecular dynamics simulations of the Na+-Cl-ion pair in DMSO have been performed to obtain the potential of mean force (PMF) and the mean force between the Na+ and the C1-ions at room temperature.The reaction field method has been used to estimate the effect of the long-range interactions. The results obtained are compared with the reported potential of mean force of Na+-Cl-ion pair in water. The mean force potential in DMSO shows that the contact ion pair (CIP) is much stabler than the solvent-separated ion pair (SSIP), whereas in water, the SSIP is as stable as the CIP. The barrier for crossing from the contact ion pair to the solvent-separated ion pair in DMSO is much larger than the corresponding value in water, whereas the barriers for crossing from the SSIP to the CIP are similar in both these solvents. The density profiles of all the interaction sites around the ion pair at the first minimum in the PMF have also been presented.
The dynamics of association of Na + -Cl -, Na + -Na + , and Cl --Cl -ion pairs in liquid dimethyl sulfoxide is studied by using the method of constrained molecular dynamics. Mean force potentials are employed to investigate the role of the solvent on the ion pairs. Friction kernels for the relative dynamics of the ion pairs have been evaluated at several interionic distances. Kramers and Grote-Hynes theories are applied to understand the passage of the ion pairs across the potential energy barrier existing between a contact ion pair and a solvent-separated ion pair. Transmission coefficients for the Na + -Cl -ion pair calculated from the above theories are in good agreement with the direct computer simulation results. The magnitudes of the squares of the nonadiabatic barrier frequencies are very large, and these confirm a polarization caging of the reactant ion pairs by the large solvent molecules.
Targeted molecular dynamics simulations were used to study the conformational transition of influenza hemagglutinin (HA) from the native conformation to putative fusogenic or postfusion conformations populated at low pH. Three pathways for this conformational change were considered. Complete dissociation of the globular domains of HA was observed in one pathway, whereas smaller rearrangements were observed in the other two. The fusion peptides became exposed and moved toward the target membrane, although occasional movement toward the viral membrane was also observed. The effective energy profiles along the paths show multiple barriers. The final low-pH structures, which are consistent with available experimental data, are comparable in effective energy to native HA. As a control, the uncleaved precursor HA0 was also forced along the same pathway. In this case both the final energy and the energy barrier were much higher than in the cleaved protein. This study suggests that 1) as proposed, the native conformation is the global minimum energy conformation for the uncleaved precursor but a metastable state for cleaved HA; 2) the spring-loaded conformational change is energetically plausible in full-length HA; and 3) complete globular domain dissociation is not necessary for extension of the coiled coil and fusion peptide exposure, but the model with complete dissociation has lower energy.
The potentials of mean force (PMFs) and the dynamics of Na+-Na+, Na+-Cl-, and Cl--Cl-ion pairs in DMSO have been obtained by using the technique of constrained molecular dynamics simulation. The long range potentials are estimated by using the reaction field method. The PMFs of these ion pairs in DMSO are compared with the reported potentials of mean force of these ion pairs in water. The Na+-Na+ and the Cl--Cl-PMFs are repulsive throughout. In the case of the Na+-Na+ ion pair, the PMF shows a shallow minimum at 3.6 8, while the Cl--Cl-PMF decays monotonically. The Na+-Cl-mean force potential shows a deep minimum corresponding to a contact ion pair (CIP) at 2.6 8, and a much shallower solvent separated ion pair (SSIP) at 7.2 8,. The trajectories of the ion pairs in DMSO are initiated in the regions of the minima and the maxima of the PMFs. It is found that the Na+-Cl-and Na+-Na+ ion pairs are very long lived and do not readily separate from their first minima at 2.6 and 3.6 8,, respectively. The trajectories initiated at the local maximum of the PMF of the Na+-Cl-ion pair tend to move from the SSIP to the CIP region. The Na+-Na+ ion pair trajectories initiated at the local maximum at 4.9 8, move outward in spite of the local minimum at 3.6 8, being 2 kcallmol below the local maximum.
A molecular dynamics simulation of ferrous and ferric ions in
water has been performed to study the
mutual orientations of the
[Fe(H2O)6]2+ and
[Fe(H2O)6]3+ complexes at
a reactive separation of 5 Å in water. The
study shows that although the conventional 3-fold 3-fold approach of
the two hexaaquo octahedral complexes is the
most dominant, the C
3 axes facing each other on
the two complexes are not directed along the
Fe2+−Fe3+ axis in
aqueous solution. The extent of the dominance of different mutual
orientations is presented.
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