Redox reactions are crucial to biological processes that protect organisms against oxidative stress. Metalloenzymes, such as cytochrome c peroxidases which reduce excess hydrogen peroxide into water in the periplasm of multiple bacterial organisms, play a key role in detoxification mechanisms. While accurate computational tools can be used to simulate ground state redox potentials in biomolecules, adapting such approaches to properly describe redox reactions in transition metal complexes, particularly in hemes in heterogeneous protein environments, remains a significant challenge. Here we present the results of polarizable hybrid QM/MM studies of the reduction potentials of two heme sites in the cytochrome c peroxidase of Nitrosomonas europaea. The simulated redox potential of the catalytic site Low Potential (LP) is in good agreement with the experiment, while for the High Potential (HP) heme the computational estimate significantly overestimate the experimental value. We have found that environment polarization shifts the computed value of the redox potential of the catalytic LP heme by 1.3 V, while it does not affect that of the non-catalytic High Potential (HP) heme. We demonstrate that it is necessary to account for mutual polarization of heme site and the protein environment when describing redox processes, particularly those that involve more charged heme sites. We have explored the role of various factors such as heme geometries, axial ligands, propionate side chains, and electrostatic field of the protein in tuning the redox potentials of hemes in NeCcP. The fluctuations in computed vertical ionization and electron attachment energies are predominantly affected by fluctuations in the electrostatic field of the environment but not by fluctuations in heme geometries. We attribute the difference in computed LP and HP heme reduction potentials of 0.05 V and 1.15 V, respectively, to different axial ligands and electrostatic interactions of the hemes with the protein environment. / 2023-06-30T00:00:00Z

Carbon nanotubes have been regarded as ideal building blocks for nanoelectronics and multifunctional nanocomposites due to their exceptional strength, stiffness, flexibility, as well as their excellent electrical properties. However, carbon nanotube itself has limitations to fulfill the practical application needs: 1) an individual carbon nanotube has a low density of states at the Fermi level, and thus its conductivity is only comparable to moderate metals but lower than that of copper. 2) Metallic and semiconducting nanotubes are inherently mixed together from the synthesis, and the selection/separation is very difficult with very low efficiency. 3) Carbon nanotubes alone cannot be used in practical application and a bonding material is normally needed as the join material for actual devices. In this work, we fundamentally explored the possibility that metals (Cu, Al) could tailor carbon nanotube’s electronic structure and even transit it from semiconducting to metallic, thus skipping the selection between the metallic and the semiconducting CNTs. We also found out a novel way to enhance a semiconducting CNT system’s conductance even better than that of a metallic CNT system. All these researches are done under density functional theory (DFT) frame in conjunction with non-equilibrium Green functions (NEGF). At first we studied the adsorbed copper’s influence on the electronic properties of CNT (10, 0) and CNT (5, 5). Results indicate that both the Density of States (DOS) and the transmission coefficients of CNT (5,5) /Cu have been increased. For CNT (10,0)/Cu, the band gap has been shrank, which means the improved conducting properties by the incorporation of copper . iv As a further case, semiconductor SWCNT (10, 0) with more adsorbed copper chains outside has been studied. 1, 4, 5 and 6 Cu chains have been added onto the carbon nanotube (10,0), and the adsorption of 6 Cu chains finally lead to the transform of the system from semiconducting to metallic. Considering the confining effect, the case that Cu filled into CNT (10, 0) is also studied. It is found that the filled copper chains could modify the system to be metallic more efficiently than the adsorbed Cu chain. Similarly, Al adsorbed on CNT (10, 0) is also studied, and it is found that Al has a better efficiency than copper in tuning the semiconducting CNT to metallic. The existing chemical bonds between the CNT and Al atoms may account for this higher efficiency. In addition, the resultant conductivity of the Al/CNT system is better than that of Cu/CNT system. The Cu/CNT (5,5)+Cu/Cu junction, as another realistic device setup, has been studied in terms of the conductance. The results show that the incorporation of Cu would enhance the conductance of the Cu/CNT/Cu system due to the interaction between Cu and the CNT.

Motivated by our frustration with the lack of quantum chemistry methods for strongly-correlated open-shell systems, we develop quantitative methods for computing the electronic structure of such systems and qualitative tools for analyzing their chemical properties and reactivity. Specifically, we present a modern framework for performing sparse configuration interaction (CI) computations with arbitrary (Slater determinant) N-electron basis sets, using restricted or generalized spin-orbitals, and including computation of spin-polarized 1- and 2- electron reduced density matrices (RDMs). This framework is then used to implement the flexible ansätze for N-electron CI (FanCI) method more efficiently, via increased vectorization in the FanCI equations and use of sparse CI algorithms. We also extended the FanCI approach, including least-squares and stochastic optimization techniques, the computation of spin-polarized 1- and 2- electron RDMs, and transition energies (ionization potentials, electron affinities, and excitation energies). We use these tools to compare various open-shell CI methods and FanCI methods based on various antisymmetrized product of nonorthogonal geminals ansätze. To translate the vast amount of quantitative data present in the energies and (spin-polarized) density matrices of multiple open-shell states, we present a new, internally consistent and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT) that reduces to a sensible formulation of spin-free CDFT in an appropriate limit. Using this framework, we were able to generalize the (non-spin-polarized) Parr function. We can also, using this framework, construct promolecules with proatoms having non-integer charges and multiplicities. Finally, we describe an equations-of-motion-based method for computing spin-polarized reactivity descriptors of a chemical system from only the ground state energy and the 1- and 2- electron RDMs from a single-point electronic structure computation, and show some benchmark computations for this method based on various CI and FanCI electronic structure methods. / Thesis / Doctor of Philosophy (PhD)

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24634号 / 工博第5140号 / 新制||工||1982(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 佐藤 啓文, 教授 佐藤 徹, 教授 松田 建児 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

There are a lot of interesting problems in surface chemistry where quantum chemistry could give great insight, like reaction mechanisms in heterogeneous catalysis, the effect of surface functionalization on semiconductors, or the influence of defects on the reactivity of crystal surfaces. Plane wave based methods applied to crystals cannot handle problems that are localized in nature like surface defects and adsorbates. On the other hand, molecular electronic structure techniques, which describe these effects and the locality of the electronic correlation well, are too computationally expensive to use on these systems. In this work, we introduce translationally-transformed coupled-cluster (TT-CC) theory, a new electronic structure method that incorporates the periodicity of crystals and the locality of electronic correlation. This is accomplished by encoding the periodicity into the amplitudes, instead of using plane waves, in order to be able to use a local basis to reflect the decay of the electronic correlation at sufficiently large distances. This avoids the calculation of redundant amplitudes. Perfectly periodic surfaces are envisioned as reference wavefunctions for localized defects and chemical reactions. The working equations in one dimension are derived starting from the amplitude equations of conventional coupled cluster singles and doubles (CCSD) on an infinite system and rearranging them such that the distance to an anonymous cell is an explicit degree of freedom, L. The formally infinite summations can be truncated by systematically neglecting numerically insignificant amplitudes. The generalization of the amplitude equations to higher dimensions is straightforward, albeit laborious. We show a general strategy to incorporate defects. These will be subjects of future dissertations. We present a proof of principle for 1-dimensional chemical systems of increasing size (He, H2, Be, Ne and N2) using the 6-31G basis set. We compute the energies, with TT-CCSD, at different distances and compared them against the perfectly periodic intensive energy (PPIE) using conventional CCSD. All results, up to L=3, show that the energies of TT-CCSD converge to the PPIE. For neon, TT-CCSD shows an error of -6.2x10-6 Eh per cell against the PPIE at the bonding distance with the potential computational cost of 7 cells using CCSD, as an upper bound. For nitrogen, TT-CCSD shows an error of -2.2x10-9 Eh at 7.5 Å per cell with the same potential cost as upper bound.

Kohn-Sham density functional theory is a rigorous formulation of many-electron quantum mechanics which, for practical purposes, requires approximation of one term in its total energy expression: the exchange-correlation energy. This work elucidates systematic methods for constructing approximations to the exchange-correlation energy solely from first-principles physics. We review the constraints that can be built into approximate density functionals, and use thermochemical data to argue that satisfaction of these constraints permits a more general description of electronic matter. Contact with semiclassical physics is made by studying the turning surfaces of Kohn-Sham potentials in solids. Perfect metals and covalently-bound, narrow-gap insulators do not have turning surfaces at equilibrium, but do under expansive strain. Wide-gap insulators, ionic crystals, and layered solids tend to have turning surfaces at equilibrium. Chemical bonds in solids are classified using the turning surface radii of its constituent atoms. Depletion of the charge density, such as near a monovacancy in platinum, is shown to produce a turning surface. Further, this work demonstrates why generalized gradient approximations (GGAs) are often able to describe some properties of sp-bonded narrow-gap insulators well. A Laplacian-level pure-density functional is developed with the goal of describing metallic condensed matter. This functional is derived from the r2SCAN orbital-dependent meta-GGA, and reduces its tendency to over-magnetize ferromagnets; improves its description of the equation of state properties of alkali metals; and improves its description of intermetallic thermodynamics. It is constructed to enforce the fourth-order exchange gradient expansion constraint (not satisfied by r2SCAN), and a few free parameters are fitted to paradigmatic metallic systems: jellium surfaces and closed-shell jellium clusters. Last, we modify an exchange-correlation kernel that describes the density-density response of jellium to better satisfy known frequency sum rules. We also constrain the kernel to reproduce the correlation energies of jellium, and compare it to a wide variety of common kernels in use for linear response, time-dependent density functional theory calculations. / Physics

Electron-driven processes lie at the core of a large variety of physical, biological, and chemical phenomena. Despite their crucial roles in science and technology, detailed description of these processes remains a significant challenge, and there is a need for the development of accurate and efficient computational tools that enable predictive simulation. This work is focused on the development of novel software tools and methodologies aimed at two classes of electron-mediated processes: (i) electron-molecule scattering, and (ii) charge transfer in proteins. The first major focus of this thesis is the electronic structure of autoionizing electronic resonances. The theoretical description of these metastable states is intractable by means of conventional quantum chemistry techniques, and specialized techniques are required in order to accurately describe their energies and lifetimes. In this work, we have utilized the complex absorbing potential (CAP) method, and describe three developments which have advanced the applicability, efficiency, and accessibility of the CAP methodology for molecular resonances: (1) implementation and investigation of the smooth Voronoi potential (2) implementation of CAP in the projected scheme, and (3) development of the OpenCAP package, which extends the CAP methodology to popular electronic structure packages. The second major focus is the identification of electron and hole transfer (ET) pathways in biomolecules. Both experimental and theoretical inquiries into electron/hole transfer processes in biomolecules generally require targeted approaches, which are complicated by the existence of numerous potential pathways. To this end, we have developed an open-source web platform, eMap, which exploits a coarse-grained model of the protein crystal structure to (1) enable pre-screening of potentially efficient ET pathways, and (2) identify shared pathways/motifs in families of proteins. Following introductory chapters on motivation and theoretical background, we devote a chapter to each new methodology mentioned above. The open-source software tools discussed herein are under active development, and have been utilized in published work by several unaffiliated experimental and theoretical groups across the world. We conclude the dissertation with a summary and discussion of the outlook and future directions of the OpenCAP and eMap software packages.

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