Computational Infrared Spectroscopy: Reproducing Kernel- and Multipolar-Based Force Field Simulations for Site-Selective Dynamics of Proteins

Characterizing the structural and functional dynamics of complex systems in the condensed phase requires fine spatial and/or temporal resolution which is a challenging problem, demanding vibrational probes that confer possible functional and steric variation on local properties. Vibrational time occurs in the femtosecond domain and frequencies are dependent on spatial arrangement and the characteristics of the constituent atoms. Therefore, vibrational spectroscopy has become an essential tool to study the structure and dynamics of various biological systems at the molecular level. However, achieving site-specific information on biological molecules of interest, such as proteins, is impossible in many cases or problematic to rely on the intrinsic vibrational modes. To overcome this limitation, the focus of this work is the development and application of several intrinsic backbone and side chain vibrational probes that can be easily incorporated into proteins and be used to site-specifically investigate their structural or environmental properties using reproducing kernel- and multipolar-based force field simulations

First-Principles Studies Of Solar Cell Materials: Absorption, Carrier Lifetime And Non-Linear Optical Effect

The next generation solar cell materials have attracted tremendous research to improve their performance. In these materials, chalcogenides materials, inorganic perovskite and newly developed organometal halide perovskite have demonstrated their potential usage as solar cells owing to their exceptional properties to absorb the light and transform the light energy to current. Hence, understanding and improving these properties can promote further material design strategies for higher performance but lower the cost. Density functional theory is a widely used accurate calculation method to compute various physical properties of a material in an efficient way. In this thesis, we mainly use the density functional theory method to explore the light-matter interaction and its effect to the material\u27s application as a solar cell. Alkali-metal chalcogenides have been found to exhibit appropriate band gaps for solar cells. We find that the volume compression can substantially enhance the optical dielectric function and the absorption coefficient intrinsically. The density function calculation and the tight-binding model show that this structure-property relation is mainly owing to the wavefunction phase change by compression, where the one-dimensional atomic chains play a significant role to relate the optical absorption and the structural change. But the high absorption does not guarantee high power conversion efficiency. This is because the excited carrier need to diffuse to the electrodes before they recombine. Organometal halide perovskites are found to have very large diffusion length and the long carrier lifetime. But the mechanism for such phenomena is still unknown. Here, by studying the structural change to the band structure and spin using CH3NH3PbI3 as an example, we find that the strong Rashba effect contributes to the long carrier lifetime by creating spin-forbidden electronic transitions, which slows down the radiative recombination and enhance the carrier lifetime. Furthermore, to study the spatial disorder effect to the electronic structure, we develop a large-scale tight-binding model which can highlight the structural disorder but still compute the band structure efficiency for very large systems. We find that the spatial disorder can create localized changes. These charge localization are spatially separated for valence band minimum and conduction band maximum. Therefore, their recombination will be further slowed down due to such spatial separation. In addition to these solar cell mechanism, we also studied the non-linear optical effect (bulk photovoltaic effect) in inorganic semiconductors. In this thesis, I use the example of CH3NH3PbI3 to illustrate its bulk photovoltaic effect responses. It is found that this material can generate more than three times large photo-current than the prototypical material BiFeO3, although its polarization is only less than one tenth of BiFeO3. We think this is due to its delocalized electronic structure of the band edges. The effect of Cl to the bulk photovoltaic response is also studied, we find that the apical substitution of I to Cl can enhance the response owing to the larger polarization. The bulk photovoltaic response of other materials such as LiAsSe2, BiFeO3 are compared, and we generalize the strategies to design new materials with better performance

Electronic Structure Calculation by First Principles for Strongly Correlated Electron Systems

Recent trends of ab initio studies and progress in methodologies for electronic structure calculations of strongly correlated electron systems are discussed. The interest for developing efficient methods is motivated by recent discoveries and characterizations of strongly correlated electron materials and by requirements for understanding mechanisms of intriguing phenomena beyond a single-particle picture. A three-stage scheme is developed as renormalized multi-scale solvers (RMS) utilizing the hierarchical electronic structure in the energy space. It provides us with an ab initio downfolding of the global band structure into low-energy effective models followed by low-energy solvers for the models. The RMS method is illustrated with examples of several materials. In particular, we overview cases such as dynamics of semiconductors, transition metals and its compounds including iron-based superconductors and perovskite oxides, as well as organic conductors of kappa-ET type.Comment: 44 pages including 38 figures, to appear in J. Phys. Soc. Jpn. as an invited review pape

Density Functional Theory

Density Functional Theory (DFT) is a powerful technique for calculating and comprehending the molecular and electrical structure of atoms, molecules, clusters, and solids. Its use is based not only on the capacity to calculate the molecular characteristics of the species of interest but also on the provision of interesting concepts that aid in a better understanding of the chemical reactivity of the systems under study. This book presents examples of recent advances, new perspectives, and applications of DFT for the understanding of chemical reactivity through descriptors forming the basis of Conceptual DFT as well as the application of the theory and its related computational procedures in the determination of the molecular properties of different systems of academic, social, and industrial interest

The design of a catalytic oxidative dimerization-cyclization system

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The kinetics of cycloaddition by fluoroolefins

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Beyond Density Functional Theory: the Multiconfigurational Approach to Model Heterogeneous Catalysis

Catalytic processes are crucially important for many practical chemical applications. Heterogeneous catalysts are especially appealing because of their high stability and the relative ease with which they may be recovered and reused. Computational modeling can play an important role in the design of more catalytically active materials through the identification of reaction mechanisms and the opportunity to assess hypothetical catalysts in silico prior to experimental verification. Kohn-Sham density functional theory (KS-DFT) is the most used method in computational catalysis because it is affordable and it gives results of reasonable accuracy in many instances. Furthermore, it can be employed in a “black-box” mode that does not require significant a priori knowledge of the system. However, KS-DFT has some limitations: it suffers from self-interaction error (sometime referred to as delocalization error), but a greater concern is that it provides an intrinsically single-reference description of the electronic structure, and this can be especially problematic for modeling catalysis when transition metals are involved. In this perspective, we highlight some noteworthy applications of KS-DFT to heterogeneous computational catalysis, as well as cases where KS-DFT fails accurately to describe electronic structures and intermediate spin states in open-shell transition metal systems. We next provide an introduction to state-of-the-art multiconfigurational (MC; also referred to as multireference (MR)) methods and their advantages and limitations for modeling heterogeneous catalysis. We focus on specific examples to which MC methods have 2 been applied and discuss the challenges associated with these calculations. We conclude by offering our vision for how the community can make further progress in the development of MC methods for application to heterogeneous catalysis

Helical Organic and Inorganic Polymers

Despite being a staple of synthetic plastics and biomolecules, helical polymers are scarcely studied with Gaussian-basis-set {\it ab initio} electron-correlated methods on an equal footing with molecules. This article introduces an {\it ab initio} second-order many-body Green's-function [MBGF(2)] method with nondiagonal, frequency-dependent Dyson self-energy for infinite helical polymers using screw-axis-symmetry-adapted Gaussian-spherical-harmonics basis functions. Together with the Gaussian-basis-set density-functional theory for energies, analytical atomic forces, translational-period force, and helical-angle force, it can compute correlated energy, quasiparticle energy bands, structures, and vibrational frequencies of an infinite helical polymer, which smoothly converge at the corresponding oligomer results. These methods can handle incommensurable structures, which have an infinite translational period and are hard to characterize by any other method, just as efficiently as commensurable structures. We apply these methods to polyethylene ($2/1$ helix), polyacetylene (Peierls' system), and polytetrafluoroethylene ($13/6$ helix) to establish the quantitative accuracy of MBGF(2)/cc-pVDZ in simulating their (angle-resolved) ultraviolet photoelectron spectra, and of B3LYP/cc-pVDZ or 6-31G** in reproducing their structures, infrared and Raman band positions, phonon dispersions, and (coherent and incoherent) inelastic neutron scattering spectra. We then predict the same properties for infinitely catenated chains of nitrogen or oxygen and discuss their possible metastable existence under ambient conditions. They include planar zigzag polyazene (N$_2$)$_x$ (Peierls' system), $11/3$-helical isotactic polyazane (NH)$_x$, $9/4$-helical isotactic polyfluoroazane (NF)$_x$, and $7/2$-helical polyoxane (O)$_x$ as potential high-energy-density materials

On the Surface Restructuring of Highly Dilute Alloys and its Effects on Catalytic Performance

Recent studies have shown that highly dilute alloys of platinum group metals (PGMs: Pt, Rh, Ir and Pd) with coinage metals (Cu, Au, and Ag) serve as highly selective and coke–resistant catalysts in a number of important chemical reactions. These materials are composed of trace amounts of a PGM or Ni, whose atoms are embedded in a coinage metal surface, and their catalytic behaviour is governed by the size and shape of the surface clusters of PGM atoms. Therefore, establishing a means of control over the topological architecture of highly dilute alloy surfaces is crucial to achieving catalytic performance tailored to a specific application. This Thesis employs density functional theory, kinetic Monte Carlo and microkinetic modelling in order to investigate ways of manipulating the surface architecture of a number of dilute alloy surfaces towards optimal performance for key catalytic reactions. The latter include the direct dissociations of NO, CO2 and N2, and the reverse events, which are important in, among others, emission control technologies. Also examined is the potential of a Ni/Cu dilute alloy for the NO + CO chemistry, and it is demonstrated that the selectivity toward the desired products can be manipulated by tuning the size of the Ni clusters in the ensemble. The results can guide future theoretical, surface science and catalysis studies on highly dilute alloys, towards the development of superior catalysts that can efficiently accelerate chemistries of industrial significance

Computational Studies and Algorithmic Research of Strongly Correlated Materials

Strongly correlated materials are an important class of materials for research in condensed matter physics. Other than ordinary solid-state physical systems, which can be well described and analyzed by the energy band theory, the electron-electron correlation effects in strongly correlated materials are far more significant. So it is necessary to develop theories and methods that are beyond the energy band theory to describe their rich and varied behaviors. Not only are there electron-electron correlations, typically the multiple degrees of freedom in strongly correlated materials, such as charge distribution, orbital occupancies, spin orientations, and lattice structure exhibit cooperative or competitive behaviors, giving rise to rich phase diagrams and sensitive or non-perturbative responses to changes in external parameters such as temperature, strain, electromagnetic fields, etc. This thesis is divided into two parts. In the first part, we use the density functional theory (DFT) plus U correction, i.e., the DFT+U method, to calculate the equilibrium and nonequilibrium phase transitions of LuNiO3 and VO2. The effect of adding U is manifested in both materials as the change of band structure in response to the change of orbital occupancies of electrons, i.e., the soft band effect. This effect bring about competitions of electrons between different orbitals by lowering the occupied orbitals and raising the empty orbitals in energy, giving rise to multiple metastable states. In the second part, we study the dynamic mean field theory (DMFT) as a beyond band-theory method. This is a Green's function based theory for open quantum systems. By selecting one lattice site of an interacting lattice model as an open system, the other lattice sites as the environment are equivalently replaced by a set of non-interaction orbitals according to the hybridization function, so the whole system is transformed into an Anderson impurity model. We studied how to use the density matrix renormalization group (DMRG) method to perform real-time evolutions of the Anderson impurity model to study the non-equilibrium dynamics of a strongly correlated lattice system. We begin in Chapter 1 with an introduction to strongly correlated materials, density functional theory (DFT) and dynamical mean-field theory (DMFT). The Kohn-Sham density functional theory and its plus U correction are discussed in detail. We also demonstrate how the DMFT reduces the lattice sites other than the impurity site as a set of non-interacting bath orbitals. Then in Chapters 2 and 3, we show material-related studies of LuNiO3 as an example of rare-earth nickelates under substrate strain, and VO2 as an example of a narrow-gap Mott insulator in a pump-probe experiment. These are two types of strongly correlated materials with localized 3d orbitals (for Ni and V). We use the DFT+U method to calculate their band structures and study the structural phase transitions in LuNiO3 and metal-insulator transitions in both materials. The competition between the charge-ordered and Jahn-Teller distorted phases of LuNiO3 is studied at various substrate lattice constants within DFT+U. A Landau energy function is constructed based on group theory to understand the competition of various distortion modes of the NiO6 octahedra. VO2 is known for its metal-insulator transition at 68 degree C, above which temperature it's a metal and below which it's an insulator with a doubled unit cell. For VO2 in a pump-probe experiment, a metastable metal phase was found to exist in the crystal structure of the equilibrium insulating phase. Our work is to understand this novel metastable phase from a soft-band picture. We also use quantum Boltzmann equation to justify the prethermalization of electrons over the lifetime of the metastable metal, so that the photoinduced transition can be understood in a hot electron picture. Finally, in Chapters 4 and 5, we show a focused study of building a real-time solver for the Anderson impurity model out of equilibrium using the density matrix renormalization group (DMRG) method, towards the goal of building an impurity solver for nonequilibrium dynamical mean-field theory (DMFT). We study both the quenched and driven single-impurity Anderson models (SIAM) in real time, evolving the wave function written in a form with 4 matrix product states (MPS) in DMRG. For the quenched model, we find that the computational cost is polynomial time if the bath orbitals in the MPSs are ordered in energy. The same energy-ordering scheme works for the driven model in the short driving period regime in which the Floquet-Magnus expansion converges. In the long-period regime, we find that the computational time grows exponentially with the physical time, or the number of periods reached. The computational cost reduces in the long run when the bath orbitals are quasi-energy ordered, which is discussed in further detail in the thesis