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Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies.

ABSTRACT: Intercalation of urea in kaolinite was investigated using infrared spectroscopy and molecular dynamics simulation. Infrared spectroscopic results indicated the formation of hydrogen bonds between urea and siloxane/alumina surfaces of kaolinite. The carbonyl group (-C=O) of urea acted as H-acceptors for the hydroxyl groups on alumina surfaces. The amine group (-NH2) of urea functioned as H-donors interacting with basal oxygens on siloxane surfaces and/or the oxygens of hydroxyl groups on alumina surfaces. The H-bonds of urea formed with kaolinite surfaces calculated directly from molecular dynamics simulation was consistent with the infrared spectroscopic results. Additionally, MD simulations further provided insight into the interaction energies of urea with the kaolinite interlayer environment. The calculated interaction energies of urea molecules with kaolinite alumina and siloxane surfaces suggest that the intercalation of urea within kaolinite interlayers is energetically favorable. The interaction energy of urea with alumina surfaces was greater than that with siloxane surfaces, indicating that the alumina surface plays a primary role in the intercalation of kaolinite by urea. The siloxane surfaces function as H-acceptors to facilitate the intercalation of urea. The present study offers a direct view of the specific driving force involved in urea intercalation in kaolinite. The results obtained can help develop appropriate protocol to intercalate and delaminate clay layers for clay-based applications and products.

SUBMITTER: Zhang S

PROVIDER: S-EPMC5896021 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies.

Zhang Shuai S Liu Qinfu Q Gao Feng F Li Xiaoguang X Liu Cun C Li Hui H Boyd Stephen A SA Johnston Cliff T CT Teppen Brian J BJ

The journal of physical chemistry. C, Nanomaterials and interfaces 20161214 1

Intercalation of urea in kaolinite was investigated using infrared spectroscopy and molecular dynamics simulation. Infrared spectroscopic results indicated the formation of hydrogen bonds between urea and siloxane/alumina surfaces of kaolinite. The carbonyl group (-C=O) of urea acted as H-acceptors for the hydroxyl groups on alumina surfaces. The amine group (-NH<sub>2</sub>) of urea functioned as H-donors interacting with basal oxygens on siloxane surfaces and/or the oxygens of hydroxyl groups ...[more]

PMID: 29657660

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Project description:We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C?O and (13)C?(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ??/4, -?/4, Y, Z? polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for ?+, ?, and ppII, and the polarizable Drude-2013 predicted dominating ? structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

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Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies.

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Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies.

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