Development and application of QM/MM methods to study the solvation effects and surfaces

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Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize the ... continued below

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167 p.

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Dibya, Pooja Arora January 1, 2010.

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This thesis or dissertation is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this document can be viewed below.

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  • Ames Laboratory
    Publisher Info: Ames Laboratory (AMES), Ames, IA (United States)
    Place of Publication: Ames, Iowa

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Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize the computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work. Chapter 2 illustrates the methodology of the interface of the EFP method with the configuration interaction with single excitations (CIS) method to study solvent effects in excited states. Chapter 3 discusses the study of the adiabatic electron affinity of the hydroxyl radical in aqueous solution and in micro-solvated clusters using a QM/EFP method. Chapter 4 describes the study of etching and diffusion of oxygen atom on a reconstructed Si(100)-2 x 1 surface using a hybrid QM/MM embedded cluster model (SIMOMM). Chapter 4 elucidates the application of the EFP method towards the understanding of the aqueous ionization potential of Na atom. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 6.

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167 p.

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  • Report No.: IS--T 2584
  • Grant Number: AC02-07CH11358
  • DOI: 10.2172/985160 | External Link
  • Office of Scientific & Technical Information Report Number: 985160
  • Archival Resource Key: ark:/67531/metadc1013016

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • January 1, 2010

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  • Oct. 14, 2017, 8:36 a.m.

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  • Nov. 2, 2017, 3:07 p.m.

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Dibya, Pooja Arora. Development and application of QM/MM methods to study the solvation effects and surfaces, thesis or dissertation, January 1, 2010; Ames, Iowa. (digital.library.unt.edu/ark:/67531/metadc1013016/: accessed April 27, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.