Strength Of Short-range Interaction Research Articles

Importance of van der Waals effects on the hydration of metal ions from the Hofmeister series.

The van der Waals (vdW) interaction plays a crucial role in the description of liquid water. Based on ab initio molecular dynamics simulations, including the non-local and fully self-consistent density-dependent implementation of the Tkatchenko-Scheffler dispersion correction, we systematically studied the aqueous solutions of metal ions (K+, Na+, and Ca2+) from the Hofmeister series. Similar to liquid water, the vdW interactions strengthen the attractions among water molecules in the long-range, leading to the hydrogen bond networks softened in all the ion solutions. However, the degree that the hydration structure is revised by the vdW interactions is distinct for different ions, depending on the strength of short-range interactions between the hydrated ion and surrounding water molecules. Such revisions by the vdW interactions are important for the understanding of biological functionalities of ion channels.

Numerical approach for finite volume three-body interaction

In present work, we study an numerical approach to one dimensional finite volume three-body interaction, the method is demonstrated by considering a toy model of three spinless particles interacting with pair-wise $\delta$-function potentials. The numerical results are compared with the exact solutions of three spinless bosons interaction when strength of short-range interactions are set equal for all pairs.

Analysis of hysteretic spin transition and size effect in 3D spin crossover compounds investigated by Monte Carlo Entropic sampling technique in the framework of the Ising-type model

In spin crossover (SCO) systems, the shape of the hysteresis curves are closely related to the interactions between the molecules, which these play an important role in the response of the system to an external parameter. The effects of short-range interactions on the different shape of the spin transition phenomena were investigated. In this contribution we solve the corresponding Hamiltonian for a three-dimensional SCO system taking into account short-range and long-range interaction using a biased Monte Carlo entropic sampling technique and a semi-analytical method. We discuss the competition between the two interactions which governs the low spin (LS) - high spin (HS) process for a three-dimensional network and the cooperative effects. We demonstrate a strong correlation between the shape of the transition and the strength of short-range interaction between molecules and we identified the role of the size for SCO systems.

Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges

An experimental approach to evaluate the net binding free energy of buried hydrogen bonds and salt bridges is presented. The approach, which involves a modified multiple-mutant cycle protocol, was applied to selected interactions between TEM-1-β-lactamase and its protein inhibitor, BLIP. The selected interactions (two salt bridges and two hydrogen bonds) all involving BLIP-D49, define a distinct binding unit. The penta mutant, where all side-chains constructing the binding unit were mutated to Ala, was used as a reference state to which combinations of side-chains were introduced. At first, pairs of interacting residues were added allowing the determination of interaction energies in the absence of neighbors, using double mutant cycles. Addition of neighboring residues allowed the evaluation of their cooperative effects on the interaction. The two isolated salt bridges were either neutral or repulsive whereas the two hydrogen bonds contribute 0.3 kcal mol −1 each. Conversely, a double mutant cycle analysis of these interactions in their native environment showed that they all stabilize the complex by 1–1.5 kcal mol −1. Examination of the effects of neighboring residues on each of the interactions revealed that the formation of a salt bridge triad, which involves two connected salt bridges, had a strong cooperative effect on stabilizing the complex independent of the presence or absence of additional neighbors. These results demonstrate the importance of forming net-works of buried salt bridges. We present theoretical electrostatic calculations which predict the observed mode of cooperativity, and suggest that the cooperative networking effect results from the favorable contribution of the protein to the interaction. Furthermore, a good correlation between calculated and experimentally determined interaction energies for the two salt bridges, and to a lesser extent for the two hydrogen bonds, is shown. The data analysis was performed on values of ΔΔ G K d ‡ which reflect the strength of short range interactions, while ΔΔ G K D ° values which include the effects of long range electrostatic forces that alter specifically ΔΔ G K a ‡ were treated separately.