Diffusional Encounter Rate Constants for Xanthone and 2-Naphthoic Acid by Flash Photolysis Experiments and Brownian Dynamics Simulations: Substantial Effects of Polarizability of the Triplet State

Stachurska, Karolina; Grochowski, Paweł; Antosiewicz, Jan

doi:10.1021/acs.jpcb.9b07989

Cited by 1 publication

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“…On the other hand, even our simplified Brownian dynamics approach is useful and enables reliable interpretation of experimental data. 58 …”

Section: Materials and Methodsmentioning

confidence: 99%

“…However, employment of more sophisticated description of the hydrodynamic interactions , can hardly be used in Brownian dynamics simulations in three-dimensional Cartesian space , because it would make the time necessary to complete the results unacceptably long. On the other hand, even our simplified Brownian dynamics approach is useful and enables reliable interpretation of experimental data …”

Section: Materials and Methodsmentioning

confidence: 99%

“…On the other hand, even our simplified Brownian dynamics approach is useful and enables reliable interpretation of experimental data. 58 To obtain diffusional encounter rate constants from BD simulations with the UHBD program, one computes and then analyzes many trajectories of one reactant diffusing toward its partner "receptor" under the influence of electrostatic intermolecular forces and the random forces mimicking the influence of the bombardment by the solvent molecules. The computation of the diffusional encounter rate constants is based on the ratio of trajectories ended with the "reaction" to the total number of trajectories.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Searching for Hydrodynamic Orienting Effects in the Association of Tri-N-acetylglucosamine with Hen Egg-White Lysozyme

2021

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Using stopped-flow fluorometry, we determined rate constants for the formation of diffusional encounter complexes of tri- N -acetylglucosamine (NAG 3 ) with hen egg-white lysozyme ( k a WT ) and its double mutant Asp48Asn/Lys116Gln ( k a MT ). We defined binding anisotropy, κ ≡ ( k a WT – k a MT )/( k a WT + k a MT ), and determined its ionic strength dependence. Our goal was to check if this ionic strength dependence provides information about the orienting hydrodynamic effects in the ligand-binding process. We also computed ionic strength dependence of the binding anisotropy from Brownian dynamics simulations using simple models of the lysozyme–NAG 3 system. The results of our experiments indicate that in the case of lysozyme and NAG 3 such hydrodynamic orienting effects are rather negligible. On the other hand, the results of our Brownian dynamics simulations prove that there exist molecular systems for which such orienting effects are substantial. However, the ionic strength dependence of the rate constants for the wild-type and modified systems do not exhibit any qualitative features that would allow us to conclude the presence of hydrodynamic orienting effects from stopped-flow experiments alone. Nevertheless, the results of our simulations suggest the presence of hydrodynamic orienting effects in the receptor–ligand association when the anisotropy of binding depends on the solvent viscosity.

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“…On the other hand, even our simplified Brownian dynamics approach is useful and enables reliable interpretation of experimental data. 58 …”

Section: Materials and Methodsmentioning

confidence: 99%