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Dehydration-mediated cluster formation of nanoparticles.

ABSTRACT: Drying procedure is a powerful method to modulate the bottom-up assembly of basic building component. The initially weak attraction between the components screened in a solution strengthens as the solvent evaporates, organizing the components into structures. Drying is process-dependent, irreversible, and nonequilibrated, thus the mechanism and the dynamics are influenced by many factors. Therefore, the interaction of the solvent and the elements during the drying procedure as well as the resulting pattern formations are strongly related. Nonetheless still many things are open in questions in terms of their dynamics. In this study, nanoscale dehydration procedure is experimentally investigated using a nanoparticle (NP) model system. The role of water is verified in a single NP scale and the patterns of collective NP clusters are determined. Stepwise drying procedures are proposed based on the location from which water is removed. Effective water exodus from a unit NP surface enhances the attractive interaction in nanoscale and induces heterogeneous distribution in microscale. This study provides fundamental proof of systematic relation between the dehydration process and the resultant cluster patterns in hierarchical multiscales.

SUBMITTER: Ahn S

PROVIDER: S-EPMC4468418 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Dehydration-mediated cluster formation of nanoparticles.

Ahn Sungsook S Lee Sang Joon SJ

Scientific reports 20150616

Drying procedure is a powerful method to modulate the bottom-up assembly of basic building component. The initially weak attraction between the components screened in a solution strengthens as the solvent evaporates, organizing the components into structures. Drying is process-dependent, irreversible, and nonequilibrated, thus the mechanism and the dynamics are influenced by many factors. Therefore, the interaction of the solvent and the elements during the drying procedure as well as the result ...[more]

PMID: 26077841

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Project description:In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics-molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water-independent enzyme-catalyzed reaction had a bias-corrected Jarzynski-average barrier height of approximately (6.5 kcal mol(-1) (27.2 kJ mol(-1)) for the carbinolamine formation reaction and 44.5 kcal mol(-1) (186 kJ mol(-1)) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately 15 kcal mol(-1) (62.8 kJ mol(-1)) in the forward (formation) reaction and 19 kcal mol(-1) (79.5 kJ mol(-1)) for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water-independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N-terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N-terminal amine.

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Dehydration-mediated cluster formation of nanoparticles.

Publications

Dehydration-mediated cluster formation of nanoparticles.

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