In the past two decades, myriad algorithms to elucidate the characteristics and dynamics of molecular systems have been developed for quantum computers. In this dissertation, we explore how these algorithms can be adapted to other fields, both to closely related subjects such as materials science, and more surprising subjects such as information theory. Special emphasis is placed on the Variational Quantum Eigensolver algorithm adapted to solve band structures of a periodic system; three distinct implementations are developed, each with its own advantages and disadvantages. We also see how unitary quantum circuits designed to model individual electron excitations within a molecule can be modified to prepare a quantum states strictly orthogonal to a space of known states, an important component to solve problems in thermodynamics and spectroscopy. Finally, we see how the core behavior in several quantum algorithms originally developed for quantum chemistry can be adapted to implement compressive sensing, a protocol in information theory for extrapolating large amounts of information from relatively few measurements. This body of work demonstrates that quantum algorithms developed to study molecules have immense interdisciplinary uses in fields as varied as materials science and information theory.

Beginning with a survey of functional variation methods in classical physics, we derive the Hartree-Fock theory from canonical quantization. Following a development of density functional theory, many-body perturbation theory, and other techniques of computational condensed matter physics, we perform a systematic study of metal-polyhydride impurities in T8 and T12 polyhedral oligomeric silsesquioxane (POSS) cage molecules. Second-quantized methods motivate the derivations throughout.

<p>Radical polymers bearing open-shell moieties at their pendant sites offer potential advantages in processing, stability, and optoelectronic properties compared to conventional doped conjugated polymers. The rapid development of radical-containing polymers has occurred across various applications in energy storage devices and electronic systems. However, significant gaps still exist in understanding the key structure-property-function relationships governing charge transport phenomena in these materials. Most reported radical conductors primarily rely on (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) radicals, which raises fundamental questions about the ultimate limits of charge transport capabilities and the impact of radical chemistry choice on material deficiencies. Moreover, an understanding gap persists when it comes to connecting the computable electronic features of individual units and the charge transport behavior of these materials in condensed phases. This dissertation seeks to address these gaps by developing a molecular understanding of charge transport in radical-bearing materials through a combined computational and experimental approach.</p> <p><br></p> <p>The initial stage of this dissertation investigated the impact of dimeric orientations and interactions on charge transport by conducting a density functional theory (DFT) study on a diverse set of open-shell chemistries relevant to radical conductors. The results revealed the anomalously high reorganization energies of the TEMPO radical due to strong spin-localization, which may result in inefficient charge transfer. Additionally, a significant mismatch was identified between dimeric conformations favored by intermolecular interactions and those maximizing charge transfer. This study provided new insights into the impact of steric hindrance and spin delocalization on elementary charge transfer steps and suggests opportunities for exploiting directing interactions to enhance charge transport in these materials.</p> <p><br></p> <p>Building upon these findings, we established a direct relationship between the molecular architecture and intrinsic charge transport properties. To accomplish this, single-molecule characterization methods (i.e., break junction techniques) were implemented to study the nanoscale charge transport properties of radical-containing oligomeric nonconjugated molecules. Temperature-dependent measurements and molecular modeling revealed that the presence of radicals improves tunneling at the nanoscale. Integrating open-shell moieties into nonconjugated molecular structures significantly enhances charge transport, thereby characterizing charge transport through radicals at the individual level and opening new avenues for implementing molecular engineering in the field of nanoelectronics.</p> <p><br></p> <p>To further connect the electronic properties of repeat units with the condensed-phase charge transport behavior of radical polymers, a quantum chemical study was carried out to explicitly evaluate the interplay between polymer design, open-shell chemistries, and intramolecular charge transport. After comprehensive conformational sampling of the configurational space of radical polymers, we determined their anticipated intrachain charge transport values by utilizing graph-based transport metrics. We show that charge transport in radical polymers primarily hinges on the choice of radical chemistry, which in turn affects the optimal selection of backbone chemistry and spacer group to ensure proper radical alignment and prevent undesired trap states. These findings highlight the potential for a substantial synthetic exploration in radical polymers for radical conductors.</p> <p><br></p> <p>In summary, this dissertation provides compelling evidence of radical-mediated charge transport and suggests potential design guidelines to enhance the charge transfer behavior of radical-containing polymer materials. Furthermore, these findings inform future research directions in fine-tuning molecular engineering and modular design to enable the development of radical-based materials and their end-use applications in organic electronics.</p>

The immaculate control of atoms and molecules with light is the defining trait of modern experiments in ultracold physics. The rich internal degrees of freedom afforded by molecules enrich the toolbox of precision spectroscopy for fundamental physics, and hold great promise for applications in quantum simulation and quantum information science. A vibrational molecular lattice clock with systematic fractional uncertainty at the 14th decimal place is demonstrated for the first time, matching the performance of the earliest optical atomic clocks. Van der Waals dimers of strontium are created at ultracold temperatures and levitated by an optical standing wave, whose wavelength is finely tuned to preserve the delicate molecular vibrational coherence. Guided by quantum chemistry theory refined by highly accurate frequency-comb-assisted laser spectroscopy, record-long Rabi oscillations were demonstrated between vibrational molecular states that span the entire depth of the ground molecular potential. Enabled by the narrow molecular clock linewidth, hertz-level frequency shifts were resolved, facilitating the first characterization of molecular hyperpolarizability in this context. In a parallel effort, deeply bound strontium dimers are coherently created using the technique of stimulated Raman adiabatic passage. Ultracold collisions of alkaline-earth metal molecules in the absolute ground state are studied for the first time, revealing inelastic losses at the universal rate. This thesis reports one of the most accurate measurement of a molecule's vibrational transition frequency to date, which may potentially serve as a secondary representation of the SI unit of time in the terahertz (THz) band where standards are scarce. The prototypical molecular clock lays the important groundwork for future explorations into THz metrology, quantum chemistry, and fundamental interactions at atomic length scales.

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

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.

<p dir="ltr">Chemical reaction networks govern polymer degradation and contain critical design information regarding specific susceptibilities, degradation pathways, and degradants. However, predicting reaction pathways and characterizing complete reaction networks has been hindered by high computational costs because of the vast number of possible reactions at deeper levels of network exploration. In the first section, an exploration policy based on Dijkstra's algorithm on YARP using the reaction rate as a cost function was shown to provide a tractable means of exploring the pyrolytic degradation network of a representative commodity polymer, PEG. The resulting network is the largest reported to date for this system and includes pathways out to all degradants observed in earlier mass spectrometry studies. The initial degradation pathway predictions were validated by complementary experimental analysis of pyrolyzed PEG samples by ESI-MS. These findings demonstrate that reaction network characterization is reaching sufficient maturity to be used as an exploratory tool for investigating materials degradation and interpreting experimental degradation studies.</p>

<p>Despite the unprecedented success achieved by Kohn-Sham density functional theory (KS-DFT) in the past few decades, the standard approximations used for the KS exchange-correlation functional typically lead to unacceptably large errors when applied to strongly-correlated electronic systems. Partition-DFT (P-DFT) is a formally exact reformulation of KS-DFT in which the ground-state density and energy of a system are obtained through self-consistent calculations on isolated fragments, with a partition energy introduced to account for the inter-fragment interactions. The unique advantage of this partitioning scheme lies in the fact that it adopts the electron density of fragments as the main variable, in place of the density of the entire system in KS-DFT, so that novel approximations can be constructed in terms of fragment properties. With a simple overlap approximation (OA) of the partition energy proposed for binary-partitioned systems, P-DFT is able to rectify the static correlation error caused by standard density functional approximations for strongly-correlated diatomic molecules. In this work, we first implement P-DFT on a one-dimensional (1D) real-space grid and calculate the ground-state energy and density of a series of 1D hydrogen chains using the local density approximation (LDA) as the density functional approximation for fragments. We then propose the generalized overlap approximation (GOA) and the corrected generalized overlap approximation (cGOA), which extends the applicability of OA to systems partitioned into more than two fragments. Combining LDA with cGOA leads to quantitatively correct dissociation curves of hydrogen chains. The static correlation error of LDA is suppressed by cGOA in the strongly-correlation regime when the calculations are performed in a spin-restricted manner, i.e., without the spin symmetry breaking. Additionally, GOA induces an improvement of the ground-state density upon LDA results, and hence helps P-DFT provide a better description of the density dimerization in hydrogen chains.</p>