Modularity and Twinning in Mineral Crystal Structures

The articles published in this Special Issue reprint offer a sound update of research fields where the concepts of modular crystallography are important and provide unique keys to understand and to solve problems of structural crystallography. Polytypism, polysomatism, and twinning are fertile fields of research, and their basic principles—often coupled with the OD (order-disorder) theory—are powerful tools to solve and classify related crystal structures. Research on twinning and its consequences on structure and properties of crystalline materials is cutting-edge, e.g., dealing with relations between twin walls and piezoelectricity

Development of crystallographic methods for phasing highly modulated macromolecular structures

[eng] Pathologies that result in highly modulated intensities in macromolecular crystal structures pose a challenge for structure solution. To address this issue two studies have been performed: a theoretical study of one of these pathologies, translational non- crystallographic symmetry (tNCS), and a practical study of paradigms of highly modulated macromolecular structures, coiled-coils. tNCS is a structural situation in which multiple, independent copies of a molecular assembly are found in similar orientations in the crystallographic asymmetric unit. Structure solution is problematic because the intensity modulations caused by tNCS cause the intensity distribution to differ from a Wilson distribution. If the tNCS is properly detected and characterized, expected intensity factors for each reflection that model the modulations observed in the data can be refined against a likelihood function to account for the statistical effects of tNCS. In this study, a curated database of 80482 protein structures from the PDB was analysed to investigate how tNCS manifests in the Patterson function. These studies informed the algorithm for detection of tNCS, which includes a method for detecting the tNCS order in any commensurate modulation. In the context of automated structure solution pipelines, the algorithm generates a ranked list of possible tNCS associations in the asymmetric unit, which can be explored to efficiently maximize the probability of structure solution. Coiled-coils are ubiquitous protein folding motifs present in a wide range of proteins that consist of two or more α-helices wrapped around each other to form a supercoil. Despite the apparent simplicity of their architecture, solution by molecular replacement is challenging due to the helical irregularities found in these domains, tendency to form fibers, large dimensions in their typically anisometric asymmetric units, low-resolution and anisotropic diffraction. In addition, the internal symmetry of the helices and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors, a Patterson map that indicates tNCS is present, and intensity modulations similar to those in true tNCS. In this study, we have explored fragment phasing on a pool of 150 coiled-coils with ARCIMBOLDO_LITE, an ab initio phasing approach that combines fragment location with Phaser and density modification and autotracing with SHELXE. The results have been used to identify limits and bottlenecks in coiled-coil phasing that have been addressed in a specific mode for solving coiled-coils, allowing the solution of 95% of the test set and four previously unknown structures, and extending the resolution limit from 2.5 Å to 3.0 Å

An investigation of the thermal behaviour of some ionic compounds by crystallographic and physical methods

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Aurivillius BaBi4Ti4O15 based compounds: Structure, synthesis and properties

The discovery of some Aurivillius materials with high Curie temperature or fatigue-free character suggests possible applications in high temperature piezoelectric devices or non-volatile ferroelectric random access memories. Furthermore, increasing concerns for environmental issues have promoted the study of new lead-free piezoelectric materials. Barium bismuth titanate (BaBi4Ti4O15), an Aurivillius compound, is promising candidate to replace lead-based materials, both as lead-free ferroelectric and high temperature piezoelectric. In this review paper, we report a detailed overview of crystal structure, different synthesis methods and characteristic properties of barium bismuth titanate ferroelectric materials

고용량 층상구조 산화물 기반 리튬 이차전지 양극 소재에 관한 연구

학위논문(박사) -- 서울대학교대학원 : 공과대학 재료공학부, 2021.8. 강기석.에너지 수요가 급증하고 환경 문제에 대한 인식이 제고되면서, 전기자동차 및 에너지저장시스템의 시장이 급속도로 성장하고 있다. 이와 발맞추어, 에너지 저장장치의 성능향상에 대한 수요 역시 급증하고 있다. 다양한 에너지 저장장치 중, 리튬이온 이차전지는 높은 에너지 밀도, 우수한 출력 특성 및 수명 특성으로 인하여 지난 수십 년간 이동식 전자장치와 전기자동차의 표준 에너지 장치로 활용되어 왔다. 하지만 차세대 에너지 기술로의 완전환 전환을 위해서는, 현 배터리 시스템에서 에너지 밀도의 비약적인 향상이 요구된다. 이러한 배경에서 다양한 차세대 전극을 개발하려는 시도가 이어지고 있다. 특히 리튬과잉 양극 소재 (lithium-rich layered oxides)는 에너지 밀도가 기존의 양극재보다 현저하게 높아 차세대 양극 소재로써 많은 관심을 받고 있다. 하지만 리튬과잉 양극 소재는 에너지 보존 성능 측면에서 명확한 한계가 있어, 에너지 보존 및 수명 특성을 향상시키는 것이 시급한 상황이다. 본 학위논문에서는 리튬과잉 양극재의 전압 강하 현상에 대한 이론적인 연구를 제시한다. 나아가 충·방전 동안 전극의 전기화학적 가역성을 향상시킬 수 있는 디자인 전략을 소개한다. 제 2장에서는 리튬과잉 양극소재에서 산화환원 메커니즘과 구조적 결함의 상관관계에 대한 통합적인 이론을 제시한다. 리튬 및 소듐 과잉 양극 소재의 산소 산화 환원은 전기화학적 비가역성과 전압 강하를 야기한다는 문제가 제기되어 왔다. 비가역적인 산소 환원과 구조적 결함의 현상적 상관관계에 대한 실험적 관찰에도 불구하고, 그 상관관계는 아직 이론적으로 설명되지 않았다. 본 연구는 구조적 결함, 결합 배열, 산소 산화환원 메커니즘 간의 다차원적 상관성을 종합적으로 연구한다. 본 연구는 넓은 범위의 리튬 과잉 양극 소재를 대상으로 하며, 양이온성 구조 결함과 음이온성 구조 결함을 모두 포함한다. 양이온성 구조 결함의 경우, 강한 산소-산소, 금속-산소 혼성을 강화시켜 산소를 안정시키며, 그 혼성의 정도는 산소의 전하량과 금속-산소 공유결합성에 의해 결정되는 것을 증명한다. 또한 구조결함으로 인한 산소 혼성이 구조적 가역성에 미치는 영향을 제시하며, 특히 구조내 생성되는 산소 이량체가 심각한 구조적 비가역성을 야기한다는 것을 제안한다. 본 연구는 오랜 기간 보고되어온 구조적 결함과 산소 산화환원 사이의 현상적 상관관계를 설명하며, 산소 산화 환원의 가역성을 향상시킬 수 있는 이론적 토대를 제시할 것으로 기대된다. 제 3장에서는 반복된 충방전 동안 리튬과잉 양극 소재의 구조적 가역성을 향상시킬 수 있는 전략을 제시한다. 이러한 전략은 소재의 전압강하 현상이 주로 전이금속의 비가역적인 이동에서 기인한다는 기존의 이해에 기초한다. 앞서 전이금속의 이동 자체를 줄이려는 시도가 많았지만, 이동의 열역학적 안정성 때문에 장사이클 동안의 구조 보존은 불가능 하였다. 본 연구는 구조 변화 자체를 억제하는 것이 아닌, 구조의 가역성을 높임으로써 리튬 과잉소재의 전압강하 현상을 해결한다. 니켈·망간 기반 리튬과잉 산화물의 산소 격자를 O3 형태에서 O2형태로 조절하고, 이를 통해 구조적 가역성을 상당히 향상시키면서 전압 강하 현상을 억제할 수 있음을 제시한다. X선 회절 분석, 주사투과 전자 현미경, 라만 분광법을 통해 충전 중 리튬 층으로 이동한 전이 금속이, 방전 시 원래의 자리로 가역적으로 돌아가는 것을 관찰한다. 나아가 제일 원리 계산을 통해 O2 산소 격자내 전이금속 자리와 리튬 자리가 서로 면을 공유하고, 이로 인한 반발력이 구조의 가역성에 크게 기여한다는 것을 증명한다. 본 연구는 재료의 구조를 리튬과잉 양극 소재의 전압 강하 및 전압 히스테리시스 현상을 해결하며, 구조적 가역성이 중요한 다양한 분야에 널리 적용될 수 있을 것으로 기대된다.With the advent of new market segment aiming at societal energy and environmental concerns such as electrified transportation and grid-scale energy storage applications, there has been the pressing demand for the improvements in the performance of energy storage systems. Among energy storage systems, rechargeable lithium-ion batteries have been the de facto standards for portable electronic devices and electrified transportation for decades owing to their high energy density, power capability and stable cyclability. However, the full-fledged placement of green energy technologies requires a significant breakthrough in the energy density of current battery systems, which has prompted the search for alternative battery electrode materials. In this regard, lithium-rich layered oxide electrodes have garnered tremendous research attention as a next-generation cathode system with exceptionally high energy density. But, the supply of high capacity from lithium-rich layered oxides has been known to compromise energy retention properties, thus it is of great importance to enhance the cycling performance of those electrodes. In this thesis, I present a theoretical investigation on the voltage depression problem of lithium-rich layered oxide electrodes, and propose a design strategy to improve electrochemical reversibility of electrodes during cycling. In Chapter 2, I designed a unified a theoretical picture of the relations between redox chemistry and structural disorders in lithium-rich layered oxide electrodes. Oxygen redox provides high energy density for lithium- and sodium-rich layered oxides electrodes, but simultaneously leads to electrochemical irreversibility and voltage depression. Despite the observation of the associations between the irreversible oxygen redox and structural disorders, their intrinsic relations have yet been fully understood because there has been little consideration of bonding rearrangements involved with structural disordering. In this respect, I comprehensively address the multifaceted connections between structural disorder, bonding arrangement, and oxygen redox chemistry. My work encompasses a wide range of lithium-rich electrodes in charge-transfer systems and Mott-Hubbard systems, and covers both cation and anion disorders. It is unraveled that cation disorders stabilize oxygen redox by driving strong oxygen-oxygen and/or metal-oxygen hybridization, and the nature of bonding reorganization depends on the occupancy of oxygen non-bonding states and metal-oxygen covalency. I further answer how the formation of short covalent bonds affects electrochemical and structural reversibility. And importantly, the free movement of oxygen dimer is spotted, suggesting poor structural resilience of oxygen dimers. On the other hand, anion disorder is found to compensate for the electron deficiency of oxygen network without significantly regulating bonding arrangements. My findings rationalize long-reported phenomenological correlations between structural disorders and oxygen redox, and offer a scientific basis for optimizing the reversibility of oxygen redox considering structural disorders. In Chapter 3, I present a design strategy to improve the structural reversibility of lithium-rich layered oxide electrodes during charging and discharging. There has been a consensus that the voltage decay is mainly originated from structural transformations involving irreversible cation migration. While many previous studies have succeeded in inhibiting cation migration itself to some extent, the thermodynamically spontaneous nature of cation migration requires a paradigm shift toward managing the reversibility of inevitable cation migration. I demonstrate for cobalt-free lithium-rich nickel manganese oxides that by tweaking the oxygen lattice of compounds from typical O3 to O2 staking, the reversibility of cation migration can be remarkably improved, thereby dramatically suppressing the voltage decay. Preeminent intra-cycle reversibility of cation migration is visualized via scanning transmission electron microscope, and such reversibility is proved to aid in the preservation of pristine structure over extended cycles. First-principle calculations verify that a large electrostatic repulsion between face-sharing cations restricts the movements of transition metals in the lithium layer, thereby streamlining the returning migration path of transition metals. Furthermore, I prove that the enhanced reversibility help mitigate the asymmetry of anion redox, which arises from the intra-cycle asymmetry of transition metal locations, ameliorating voltage hysteresis concurrently.Chapter 1. Introduction 1 1.1 Motivation and outline 1 1.2 References 6 Chapter 2. Trilateral correlation of structural disorder, bond covalency, and oxygen redox chemistry in lithium-rich layered oxide electrodes 9 2.1 Introduction 9 2.2 Computational details 13 2.3 Result and Discussion 15 2.3.1 Cation disordering in charge-transfer systems 15 2.3.2 Cation disordering in Mott-Hubbard systems 36 2.3.3 Reversibility and asymmetry of the oxygen redox 63 2.3.4 Anionic disorder and oxygen redox chemistry 94 2.3.5 Theoretical voltage profiles considering structural disorder 108 2.3.6 Electronic structure of electrodes 111 2.3.7 Effects of metal-oxygen decoordination on the electronic structure 114 2.3.8 Types of oxygen dimer 116 2.3.9 Cation migration in Na0.6[Li0.2Mn0.8]O2 and Na2/3[Mg1/3Mn2/3]O2 119 2.3.10 Effects of metal substitution on bond rearrangements 122 2.4 Concluding remarks 143 2.5 References 144 Chapter 3. Voltage decay and redox asymmetry mitigation by reversible cation migration in lithium-rich layered oxide electrodes 156 3.1 Introduction 156 3.2 Experimental and computational details 162 3.3 Results and discussion 167 3.3.1 Electrochemistry of O2-LLNMOs 167 3.3.2 Reversible cation migration in O2-LLNMOs 174 3.3.3 High-potential O redox behavior preserved in O2-LLNMOs 190 3.3.4 Synthesis of O2-LLNMOs 198 3.3.5 Structural characterization of O2-LLNMOs 204 3.3.6 Theoretical investigation of cation migration pathways 205 3.3.7 Partial manganese reduction during discharge 217 3.4 Concluding remarks 218 3.5 References 220 Chapter 4. Summary 231 Abstract in Korean 233박

The molecular structure of collagen

This thesis describes the study of the molecular packing and organisation of collagen molecules within a fibril. The first two chapters describe the background to the study. In Chapter 1, a review of the extracellular matrix concentrates on the structure and organisation of type I collagen. Chapter 2 summarises the theory of X-ray diffraction by fibres, and Chapter 3 describes X-ray sources and equipment used in data collection. Data treatments and data extraction methods (such as simulated annealing) are also discussed. Chapters4 and 5 present the results of the study. Chapter 4 describes the determination of the one-dimensional structure of type I collagen to 0.54 nm resolution using X-ray diffraction and isomorphous derivative phase determination. The significance of the electron density map is interpreted in light of the known amino acid sequence, showing possible variations in the nature of the helix pitch. More importantly, the conformations of the intermolecular crosslink forming non-helical telopeptides were determined. Chapter 5 provides a detailed background to the current understanding of the three dimensional packing structure of collagen, and presents the first model-independent phase determined structure of a natural fibre - the lateral packing structure of type I collagen in rat tail tendon. The data extraction methods described in Chapter 3 are employed to calculate an electron density map of anisotropic resolution, from which the 4 crosslink forming telopeptide segments within the quasi-hexagonal packing structure are identified. Conclusions are drawn concerning the nature of order/disorder within collagen fibrils and the validity of the compressed microfibril model of collagen molecular packing and organisation is discussed. Chapter 6 summaries the results and evaluates the success of the study. The potential for development of the techniques and results found for further studies are also discussed

The aperiodic nature of mullite

181 p.Different methods were applied to investigate the vacancy and Al/Si order in mullite. At first the symmetry was analysed thoroughly to derive constraints on the vacancy distribution based on crystal chemical premises. On this basis a superspace model was developed that defines the polyhedra network consisting of octahedra, tetrahedral tricluster units and tetrahedral dicluster units as a function of the modulation wave vector and the vacancy concentration. Refinements of superspace models based on synchrotron single crystal X-ray diffraction measurements indicate that in the real structure the identified pattern is present, but with a decreased degree of order. Different samples exhibit different degrees of order suggesting that mainly disordered and fully ordered mullite crystals exist. The Al/Si ordering could not be derived from symmetry constraints and the occupancy of Si could not be refined. Nevertheless, an Al/Si ordering pattern could be identified from the analysis of the displacive modulation.The dependence of the satellite reflections on the chemical composition was studied with precession electron diffraction tomography and density functional theory. This allowed to characterise the structural modulation on a new level and reveal the fundamental ordering patterns that define the crystal structure of mullite in terms of vacancy, tricluster and Al/Si order. The understanding of the crystal structure forms a new basis for future research on the properties of mullite and related applications