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## Über dieses Buch

This volume develops multiscale and multiphysics simulation methods to understand nano- and bio-systems by overcoming the limitations of time- and length-scales. Here the key issue is to extend current computational simulation methods to be useful for providing microscopic understanding of complex experimental systems. This thesis discusses the multiscale simulation approaches in nanoscale metal-insulator-metal junction, molecular memory, ionic transport in zeolite systems, dynamics of biomolecules such as lipids, and model lung system. Based on the cases discussed here, the author suggests various systematic strategies to overcome the limitations in time- and length-scales of the traditional monoscale approaches.

## Inhaltsverzeichnis

### Chapter 1. Introduction

Abstract
Many chemical and physical problems in complex systems such as nano- and bio-systems have multiscale and multiphysics characteristics. To understand these systems, we developed multiscale and multiphysics simulation methods by overcoming the limitations of time- and length-scales. Here the key issue is to extend current computational simulation methods to be useful for providing microscopic understanding of complex experimental systems. We discussed the multiscale simulation approaches in nanoscale metal-insulator-metal junction, molecular memory, ionic transport in zeolite systems, dynamics of biomolecules such as lipids, and model lung system. Based on the cases discussed here, we expect that multiscale modeling procedures will be an interdisciplinary tool that can combine the developments occurring independently across fields.
Hyungjun Kim

### Chapter 2. Negative Differential Resistance of Oligo (Phenylene Ethynylene) Self-Assembled Monolayer Systems: The Electric Field Induced Conformational Change Mechanism

Abstract
We investigate here a possible mechanism for the room temperature Negative Differential Resistance (NDR) in the Au/AN-OPE/RS/Hg self-assembled monolayer (SAM) system, where AN-OPE = 2’-amino, 5’-nitro oligo (phenylene ethynylene) and RS is a C14 alkyl thiolate. Kiehl and co-workers showed that this molecular system leads to NDR with hysteresis and sweep-rate-dependent position and amplitude in the NDR peak. To investigate a molecular basis for this interesting behavior, we combine first principles quantum mechanics (QM) and meso-scale lattice Monte Carlo (MC) methods to simulate the switching as a function of voltage and voltage rate, leading to results consistent with experimental observations. This simulation shows how the structural changes at the microscopic level lead to the NDR and sweep-rate dependent macroscopic I-V curve observed experimentally, suggesting a microscopic model that might aid in designing improved NDR systems.
Hyungjun Kim

### Chapter 3. Free Energy Barrier for Molecular Motions in Bistable [2]Rotaxane Molecular Electronic Devices

Abstract
Donor-acceptor binding of the π-electron-poor cyclophane cyclobis (paraquat-p-phenylene) (CBPQT4+) with the π-electron-rich tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) stations provides the basis for electrochemically switchable, bistable [2]rotaxanes, which have been incorporated and operated within solid state devices to form ultradense memory circuits [1, 2] and nanoelectromechanical systems. The rate of CBPQT4+ shuttling at each oxidation state of the [2]rotaxane dictates critical write-and-retention time parameters within the devices, which can be tuned through chemical synthesis. To validate how well computational chemistry methods can estimate these rates for use in designing new devices, we used molecular dynamics simulations to calculate the free energy barrier for the shuttling of the CBPQT4+ ring between the TTF and the DNP. The approach used here was to calculate the potential of mean force along the switching pathway, from which we calculated free energy barriers. These calculations find a turn-on time after the rotaxane is doubly oxidized of $$\sim\!\!10^{-7}$$ s (suggesting that the much longer experimental turn-on time is determined by the time scale of oxidization). The return barrier from the DNP to the TTF leads to a predicted lifetime of 2.1 s, which is compatible with experiments.
Hyungjun Kim

### Chapter 4. Sodium Diffusion Through Aluminum-Doped Zeolite BEA System: Effect of Water Solvation

Abstract
To investigate the effect of hydration on the diffusion of sodium ions through the aluminum-doped zeolite BEA system (Si/Al = 30), we used the grand canonical Monte Carlo (GCMC) method to predict the water absorption into aluminosilicate zeolite structure under various conditions of vapor pressure and temperature, followed by molecular dynamics (MD) simulations to investigate how the sodium diffusion depends on the concentration of water molecules. The predicted absorption isotherm shows first-order-like transition, which is commonly observed in hydrophobic porous systems. The MD trajectories indicate that the sodium ions diffuse through zeolite porous structures via hopping mechanism, as previously discussed for similar solid electrolyte systems. These results show that above 15 wt % hydration (good solvation regime) the formation of the solvation cage dramatically increases sodium diffusion by reducing the hopping energy barrier by 25% from the value of 3.8 kcal/mol observed in the poor solvation regime.
Hyungjun Kim

### Chapter 5. Experimental and Theoretical Investigation into the Correlation Between Mass and Ion Mobility for Choline and Other Ammonium Cations in N2

Abstract
A number of tertiary amine and quaternary ammonium cations spanning a mass range of 60–146 amu (trimethylamine, tetramethylammonium, trimethylethylammonium, N, N-dimethylaminoethanol, choline, N, N-dimethylglycine, betaine, acetylcholine, (3-carboxypropyl)trimethylammonium) were investigated using electrospray ionization ion mobility spectrometry. Measured ion mobilities demonstrate a high correlation between mass and mobility in N2. In addition, identical mobilities within experimental uncertainties are observed for structurally dissimilar ions with similar ion masses. For example, dimethylethylammonium (88 amu) cations and protonated N, N-dimethylaminoethanol cations (90 amu) show identical mobilities ($$1.93\,{\textrm{cm}}^2\,{\textrm{V}}^{-1}\,{\textrm{s}}^{-1}$$) though N, N-dimethylaminoethanol contains a hydroxyl functional group while dimethylethylammonium only contains alkyl groups. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical N2 molecules as the drift gas. The sensitivity of the ammonium cation collision cross-sections to the details of the ion-neutral interactions was investigated and compared to other classes of organic molecules (carboxylic acids and abiotic amino acids). The specific charge distribution of the molecular ions in the investigated mass range has an insignificant affect on the collision cross-section.
Hyungjun Kim

### Chapter 6. Structural Characterization of Unsaturated Phospholipids Using Traveling Wave Ion Mobility Spectrometry

Abstract
A number of phosphatidylcholine (PC) cations spanning a mass range of 400 to 1000 Da are investigated using electrospray ionization mass spectrometry coupled with traveling wave ion mobility spectrometry (TWIMS). A high correlation between mass and mobility is demonstrated with saturated phosphatidylcholine cations in N2. A significant deviation from this mass-mobility correlation line is observed for the unsaturated PC cation. We found that the double bond in the acyl chain causes a 5 % reduction in drift time. The drift time is reduced at a rate of ∼ 1% for each additional double bond. Theoretical collision cross-sections of PC cations exhibit good agreement with experimentally evaluated values. Collision cross-sections are determined using the recently derived relationship between mobility and drift time in TWIMS stacked ring ion guide (SRIG) and compared to estimate collision cross-sections using empiric calibration method. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical N2 molecules as the drift gas. The difference between estimated collision cross-sections and theoretical collision cross-sections of PC cations is related to the sensitivity of the PC cation collision cross-sections to the details of the ion-neutral interactions. The origin of the observed correlation and deviation between mass and mobility of PC cations is discussed in terms of the structural rigidity of these molecules using molecular dynamics simulations.
Hyungjun Kim

### Chapter 7. Interfacial Reactions of Ozone with Lipids and Proteins in a Model Lung Surfactant System

Abstract
Oxidative stresses from irritants such as hydrogen peroxide and ozone (O3) can cause dysfunction of the pulmonary surfactant (PS) in the human lung, resulting in chronic diseases of the respiratory tract. For identification of structural changes of major components of PS due to the heterogeneous reaction with O3, field induced droplet ionization (FIDI) mass spectrometry is utilized to probe the surfactant layer system. FIDI is a soft ionization method in which ions are extracted from the surface of micro liter volume droplets. We report the structurally specific oxidative changes of $$\textrm{SP-B}_{1-25}$$ (a shortened version of human surfactant protein B) and 1-palmitoyl-2-oleoyl-sn-phosphatidylglycerol (POPG) due to reaction with O3 at the air-liquid interface. We also present studies of the interfacial oxidation of $$\textrm{SP-B}_{1-25}$$ in a non-ionizable 1-palmitoyl-2-oleoyl-sn-glycerol monolayer as a model lung surfactant system, where the competitive oxidation of the two components is observed. Our results indicate that the heterogeneous reaction at the interface is different from that in the bulk phase. For example, we observe the hydroxyhydroperoxide and the secondary ozonide as major products of the heterogeneous ozonolysis of POPG. These products are metastable and difficult to observe in the bulk-phase. In addition, compared to the nearly complete homogeneous oxidation of $$\textrm{SP-B}_{1-25}$$, only a subset of the amino acids known to react with ozone is oxidized in the hydrophobic interfacial environment. Combining these experimental observations with the results of molecular dynamics simulations provides an improved understanding of the interfacial structure and chemistry of a model lung surfactant system when subject to oxidative stress.
Hyungjun Kim

### Chapter 8. Appendices

Abstract
This chapter provides appendices to support the understanding of readers. Appendices A to D contain supporting information of Chapter 2; appendices E and F contain supporting information of Chapter 3; and appendices G and H contain supporting information of Chapter 7.
Hyungjun Kim

### Backmatter

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