Electronic Structure最新文献

英文中文

Low-rank approximations to accelerate hybrid functional enabled real-time time-dependent density functional theory within plane waves 低阶近似加速平面波内混合泛函实时含时密度泛函理论

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-03-15 DOI: 10.1088/2516-1075/acc4a0

Jielan Li, Lingyun Wan, Shizhe Jiao, Wei Hu, Jinlong Yang

Real-time time-dependent density functional theory (RT-TDDFT) is a powerful tool for predicting excited-state dynamics. Herein, we combine the adaptively compressed exchange (ACE) operator with interpolative separable density fitting (ISDF) algorithm to accelerate the hybrid functional calculations in RT-TDDFT (hybrid RT-TDDFT) dynamics simulations for molecular and periodic systems within plane waves. Under this low-rank representation, we demonstrate that the ACE-ISDF enabled hybrid RT-TDDFT can yield accurate excited-state dynamics, but much faster than conventional calculations. Furthermore, we describe a massively parallel implementation of ACE-ISDF enabled hybrid RT-TDDFT dynamics simulations containing thousands of atoms (1728 atoms), which can scale up to 3456 central processing unit cores on modern supercomputers.

实时时变密度泛函理论(RT-TDDFT)是预测激发态动力学的有力工具。本文将自适应压缩交换(ACE)算子与插值可分密度拟合(ISDF)算法相结合，加速了平面波内分子和周期系统RT-TDDFT动力学模拟中的混合泛函计算。在这种低秩表示下，我们证明了ACE-ISDF支持的混合RT-TDDFT可以产生精确的激发态动力学，但比传统计算快得多。此外，我们描述了ACE-ISDF支持的混合RT-TDDFT动力学模拟的大规模并行实现，该模拟包含数千个原子(1728个原子)，可以在现代超级计算机上扩展到3456个中央处理单元核心。

引用次数: 0

The Electronic Structure of Genome Editors from the First Principles. 从第一原理看基因组编辑器的电子结构。

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-03-01 DOI: 10.1088/2516-1075/acb410

Łukasz Nierzwicki, Mohd Ahsan, Giulia Palermo

Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.

基于CRISPR-Cas9系统的基因组编辑为医学、制药、生物技术等领域铺平了新的道路。本文报道了第一性原理(ab-initio)分子动力学(MD)在CRISPR-Cas9革命中的作用，实现了对酶功能的深刻理解，为酶工程提供了有价值的见解。我们介绍了方法并解释了使用ab-initio MD模拟来表征Cas9酶RuvC结构域中DNA切割的双金属依赖机制，以及第二个催化结构域HNH如何在单个金属离子的帮助下切割目标DNA。详细描述了ab-initio MD如何与自由能方法(即热力学集成和元动力学)相结合来破坏和形成化学键，并解释了使用这些方法来确定CRISPR-Cas9中的化学景观和建立催化机制。讨论了经典方法的关键作用，解释了恒定pH MD模拟的理论和应用，用于准确预测催化残基的质子化状态。总的来说，第一性原理方法揭示了Cas9酶的电子结构，为设计具有更高催化效率或可控活性的基因组编辑工具提供了有价值的见解。

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引用次数: 1

Strain effect on the high T c superconductor YBa2Cu3O7: an ab initio study comparing bulk and monolayer models 高温超导体YBa2Cu3O7的应变效应:体模型与单层模型的从头算比较

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-02-28 DOI: 10.1088/2516-1075/acbff9

C. Yelpo, S. Favre, D. Ariosa, R. Faccio

In this work, the effect of strain on the vibrational and electronic properties of the YBa2Cu3O7 compound was studied through ab initio calculations. For this, two structural models were used: a bulk model and a surface model (a monolayer with CuO2 and BaO as the terminating layers). The phonon spectra was calculated for both structures under different levels of c axis strain. The most appreciable change occurs in the vibrational properties, and in the surface case. From the simulation of the Raman spectra, we were able to quantify the Raman shift ratio as a function of the applied strain, and analyzed its behavior in terms of the overlap population of the different bonds and the reduced mass of selected phonons. The effect of the level of deformation on the band structure and the electronic density of states is small for both structures, although more noticeable in the case of the surface model. In both cases, tendencies are observed when the fine features of the band structure are analyzed by means of the tight binding model. Due to the lower symmetry, the surface model also shows modifications of the bands related to the CuO2 planes.

本文通过从头计算研究了应变对YBa2Cu3O7化合物振动和电子性能的影响。为此，使用了两种结构模型:体模型和表面模型(以CuO2和BaO为终止层的单层)。计算了两种结构在不同c轴应变水平下的声子谱。最明显的变化发生在振动性质和表面情况。从拉曼光谱的模拟中，我们能够量化拉曼位移比作为施加应变的函数，并根据不同键的重叠人口和选定声子的减少质量来分析其行为。变形水平对能带结构和态电子密度的影响对两种结构都很小，尽管在表面模型的情况下更为明显。在这两种情况下，当用紧密结合模型分析带结构的精细特征时，都可以观察到趋势。由于较低的对称性，表面模型还显示了与CuO2平面相关的能带的修改。

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引用次数: 0

Anomalous delocalization of resonant states in graphene & the vacancy magnetic moment 石墨烯共振态的反常离域&空位磁矩

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-02-23 DOI: 10.1088/2516-1075/acdbf4

M. Leccese, R. Martinazzo

Carbon atom vacancies in graphene give rise to a local magnetic moment of σ+π origin, whose magnitude is yet uncertain and debated. Partial quenching of π magnetism has been ubiquitously reported in periodic first principles calculations, with magnetic moments scattered in the range 1.0–2.0 µ B, slowly converging to the lower or the upper end, depending on how the diluted limit is approached. By contrast, (ensemble) density functional theory calculations on cluster models neatly converge to the value of 2 μB when increasing the system size. This stunning discrepancy has sparked a debate about the role of defect–defect interactions and self-doping, and about the importance of the self-interaction-error in the density-functional-theory description of the vacancy-induced states. Here, we settle this puzzle by showing that the problem has a fundamental, mono-electronic origin which is related to the special (periodic) arrangement of defects that results when using the slab-supercell approach. Specifically, we report the existence of resonant states that are anomalously delocalized over the lattice and that make the π midgap band unphysically dispersive, hence prone to self-doping and quenching of the π magnetism. Hybrid functionals fix the problem by widening the gap between the spin-resolved π midgap bands, without reducing their artificial widths. As a consequence, while reconciling the magnetic moment with expectations, they predict a spin-splitting which is one order of magnitude larger than found in experiments.

石墨烯中的碳原子空位会产生σ+π起源的局部磁矩，其大小尚不确定，也存在争议。在周期第一性原理计算中，π磁性的部分猝灭已被普遍报道，磁矩分散在1.0–2.0µB的范围内，慢慢收敛到下端或上端，这取决于如何接近稀释极限。相比之下，聚类模型上的（系综）密度泛函理论计算巧妙地收敛到2的值 μB。这种惊人的差异引发了关于缺陷-缺陷相互作用和自掺杂的作用，以及自相互作用误差在空位诱导态的密度泛函理论描述中的重要性的辩论。在这里，我们通过证明这个问题有一个基本的单电子起源来解决这个难题，这与使用平板超晶胞方法时产生的缺陷的特殊（周期性）排列有关。具体地说，我们报道了共振态的存在，这些共振态在晶格上异常离域，使π中隙带不具有物理色散性，因此易于自掺杂和π磁性的猝灭。混合泛函通过扩大自旋分辨的π中隙带之间的间隙来解决这个问题，而不减少它们的人工宽度。因此，在调和磁矩与预期的同时，他们预测了比实验中发现的大一个数量级的自旋分裂。

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引用次数: 0

Decomposing Hofmeister effects on amino acid residues with symmetry adapted perturbation theory 用对称适配微扰理论分解氨基酸残基上的Hofmeister效应

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-02-23 DOI: 10.1088/2516-1075/acbe84

Kasimir P. Gregory, G. Webber, E. Wanless, A. Page

Hofmeister effects, and more generally specific ion effects, are observed broadly in biological systems. However, there are many cases where the Hofmeister series might not be followed in complex biological systems, such as ion channels which can be highly specific to a particular ion. An understanding of how ions from the Hofmeister series interact with the proteinogenic amino acids will assist elucidation of why some binding interactions may be favoured over others. Using symmetry adapted perturbation theory (SAPT2 + 3), the interaction energies between a selection of anions and each amino acid have been investigated. The interaction strengths become more favourable in accordance with the Hofmeister series, and also with increasing polarity of the amino acids (with the exception of the negatively charged amino acid side chains). Furthermore, the interactions are generally most favourable when they simultaneously involve the side chain and both protic moieties of the backbone. The total interaction energy in these anion–amino acid complexes is also primarily determined by its electrostatic component, in a manner proportional to the þ (‘sho’) value of the anion.

霍夫梅斯特效应，以及更普遍的特定离子效应，在生物系统中被广泛观察到。然而，在许多情况下，在复杂的生物系统中，例如对特定离子具有高度特异性的离子通道，可能不会遵循Hofmeister系列。了解Hofmeister系列离子如何与蛋白质生成氨基酸相互作用，将有助于阐明为什么某些结合相互作用可能比其他结合相互作用更受青睐。利用对称适配微扰理论（SAPT2+3），研究了一系列阴离子与每种氨基酸之间的相互作用能。根据Hofmeister系列，以及随着氨基酸极性的增加（带负电荷的氨基酸侧链除外），相互作用强度变得更有利。此外，当它们同时涉及主链的侧链和两个质子部分时，相互作用通常是最有利的。这些阴离子-氨基酸复合物中的总相互作用能也主要由其静电成分决定，其方式与阴离子的þ（“o”）值成比例。

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引用次数: 3

From defect to effect: controlling electronic transport in chevron graphene nanoribbons 从缺陷到效果:控制石墨烯纳米带中的电子输运

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-02-21 DOI: 10.1088/2516-1075/acbdd9

Kristiāns Čerņevičs, O. Yazyev

While bottom-up synthesis allows for precise control over the properties of graphene nanoribbons (GNRs), the use of certain precursor molecules can result in edge defects, such as missing benzene rings that resemble a ‘bite’. We investigate the adverse effect of the ‘bite’ defects on the electronic transport properties in three chevron-type GNRs and discover that the extent of scattering is governed by the different defect positions. Applying the concepts learned in single GNRs, we engineer defects in two nanostructures to construct prototypical components for nanoelectronics. First, we design a switch, consisting of three laterally fused fluorenyl-chevron GNRs, and place a pair of ‘bite’ defects to effectively allow the switching between four binary states corresponding to distinct current pathways. Second, we show that conscientious placement of a ‘bite’ defect pair can increase conductance between two leads in a triple chevron GNR junction. Overall, we outline how the incorporation of ‘bite’ defects affects transport properties in chevron-type nanostructures and provide a guide on how to design nanoelectronic components.

虽然自下而上的合成可以精确控制石墨烯纳米带（GNRs）的性能，但使用某些前体分子可能会导致边缘缺陷，例如类似“咬”的苯环缺失。我们研究了“咬合”缺陷对三种V型GNR中电子输运性质的不利影响，并发现散射的程度由不同的缺陷位置决定。应用在单个GNR中学到的概念，我们在两个纳米结构中设计缺陷，以构建纳米电子的原型组件。首先，我们设计了一个开关，由三个横向融合的芴人字形GNR组成，并放置一对“咬合”缺陷，以有效地允许在对应于不同电流路径的四个二元状态之间切换。其次，我们证明了在三人字形GNR结中，认真放置“咬合”缺陷对可以增加两个引线之间的电导。总之，我们概述了“咬合”缺陷的引入如何影响人字形纳米结构的传输特性，并为如何设计纳米电子元件提供了指导。

引用次数: 0

Covalency modulation enables stable Na-rich layered oxide cathodes for Na-ion batteries 共价调制使钠离子电池的富钠层状氧化物阴极稳定

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-02-08 DOI: 10.1088/2516-1075/acba6e

Xi Zhou, Manling Ding, Chen Cheng, Xiao-Hui Xia, Haolv Hu, Yihao Shen, S. Fedotov, Liang Zhang

As the analogs of Li-rich materials, Na-rich transition metal layered oxides are promising cathode materials for Na-ion batteries owing to their high theoretical capacity and energy density through cumulative cationic and anionic redox. However, most of the reported Na-rich cathode materials are mainly Ru- and Ir-based layered oxides, which limits the practical application. Herein, we report a Na-rich and Ru-doped O3-type Na1.1Ni0.35Mn0.55O2 cathode to mitigate this issue. By partially substituting Mn4+ with high-electronegativity Ru4+, the structural stability and electrochemical performance of the cathode are both greatly improved. It is validated that the high covalency of Ru–O bonds could harden the structural integrity with rigid oxygen framework upon cycling, leading to enhanced O3-P3 phase transition reversibility. Ru doping also induces an enlarged interlayer spacing to boost the Na+ diffusion kinetics for improved rate capability. In addition, benefiting from the large energetic overlap between Ru 4d and O 2p states, the reinforced Ru–O covalency enables highly reversible Ru4+/Ru5+ redox accompanied with more stable oxygen redox, leading to improved specific capacity and stability over cycling. Our present study provides a promising strategy for designing high-performance Na-rich layered oxide cathode materials through covalency modulation toward practical applications.

富钠过渡金属层状氧化物作为富锂材料的类似物，通过累积的正离子和阴离子氧化还原，具有较高的理论容量和能量密度，是钠离子电池极有前景的正极材料。然而，目前报道的富钠正极材料多以钌基和铁基层状氧化物为主，限制了其实际应用。本文报道了一种富na和掺ru的o3型Na1.1Ni0.35Mn0.55O2阴极来缓解这一问题。用高电负性的Ru4+部分取代Mn4+，大大提高了阴极的结构稳定性和电化学性能。验证了Ru-O键的高共价可以在循环过程中硬化具有刚性氧框架的结构完整性，从而增强O3-P3相变的可逆性。Ru的掺杂也导致了层间距的增大，从而提高了Na+的扩散动力学，从而提高了速率能力。此外，得益于ru4d和o2p态之间的大能量重叠，增强的Ru - O共价使得Ru4+/Ru5+具有高可逆性的氧化还原，同时伴随着更稳定的氧氧化还原，从而提高了比容量和循环稳定性。本研究为通过共价调制设计高性能富钠层状氧化物正极材料提供了一种具有实际应用前景的方法。

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引用次数: 1

High-resolution electronic and vibrational spectroscopy of small-to-medium sized molecules with ab initio potential energy surface 具有从头算势能面的中小分子的高分辨率电子和振动光谱

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-01-31 DOI: 10.1088/2516-1075/acb7b8

Soumyadip Ray, Debasish Koner, Padmabati Mondal

Electronic and vibrational spectroscopic studies of molecules are of crucial importance to characterizing a molecule and detecting the molecular species in different environments. In this review article, we summarized some important theoretical methods to calculate high-resolution electronic spectra and ro-vibrational states for small molecular systems with the inclusion of vibronic and ro-vibrational couplings, respectively. We have also reviewed a number of theoretical studies exploring some interesting organic chromophores like indole, isoalloxazine, transition metal trifluoride CoF3 and NiF3, and molecular ions like protonated rare gases and azido ions. These studies involve the calculation of spectroscopic features based on analytical potential energy surfaces (PESs) constructed using high-level ab initio energies. The topology of the PESs has been explored for these selected systems. The vibronic spectra and ro-vibrational states calculated using various theoretical methods and their comparison to available experimental results are reported in this review.

分子的电子和振动光谱研究对于表征分子和检测不同环境下的分子种类具有至关重要的意义。本文综述了计算含振动耦合和含振动耦合的小分子系统的高分辨率电子谱和无振动态的一些重要理论方法。我们还回顾了一些理论研究，探索了一些有趣的有机发色团，如吲哚，异alloxazine，过渡金属三氟化CoF3和NiF3，以及分子离子，如质子化稀有气体和叠氮离子。这些研究包括基于分析势能面(PESs)的光谱特征计算，该分析势能面是用高能级从头算能量构造的。已经为这些选定的系统探索了PESs的拓扑结构。本文报道了用各种理论方法计算的振动谱和反振动态，并与已有的实验结果进行了比较。

引用次数: 0

Accurate and efficient prediction of vibrational circular dichroism spectra of condensed-phase systems with the generalized energy-based fragmentation method 广义能量碎裂法准确有效地预测凝聚相系统的振动圆二色性光谱

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-01-10 DOI: 10.1088/2516-1075/acb1e7

Dongbo Zhao, K. Liao, Benkun Hong, Wei Li, Shuhua Li

The vibrational circular dichroism (VCD) spectra could determine the molecular chirality of condensed-phase systems, but their quantum chemistry calculations are costly. The fragment-based methods have not been applied to the VCD spectra of periodic systems yet. In this work, we have extended the generalized energy-based fragmentation (GEBF) approach to accurately and efficiently compute the VCD spectra of chiral molecular crystals under periodic boundary conditions (PBCs) and macromolecules in solutions. In this approach, the Hessian matrices, atomic polar/axial tensors of a target system, are evaluated as a linear combination of the corresponding quantities from a series of small electrostatically embedded subsystems. Comparisons of GEBF and conventional VCD spectra of two large molecules show that this approach can satisfactorily reproduce the conventional computational results. Then, we applied the PBC-GEBF method to calculate the VCD spectra of a chiral molecular crystal and two macromolecules in solutions. Our results show that the experimental VCD spectrum can be roughly reproduced in terms of both band shape and vibrational peaks. The GEBF-VCD and PBC-GEBF-VCD approaches are expected to be practical tools to investigate the chirality of molecular crystals and macromolecules in solutions.

振动圆二色性（VCD）光谱可以确定凝聚相系统的分子手性，但其量子化学计算成本高昂。基于碎片的方法尚未应用于周期系统的VCD光谱。在这项工作中，我们扩展了广义基于能量的碎裂（GEBF）方法，以准确有效地计算周期边界条件下手性分子晶体和溶液中大分子的VCD光谱。在这种方法中，Hessian矩阵，即目标系统的原子极/轴张量，被评估为来自一系列小型静电嵌入子系统的相应量的线性组合。对两个大分子的GEBF和常规VCD光谱的比较表明，该方法可以令人满意地再现传统的计算结果。然后，我们应用PBC-GEBF方法计算了溶液中一个手性分子晶体和两个大分子的VCD光谱。我们的结果表明，实验VCD光谱可以从带形和振动峰两个方面粗略地再现。GEBF-VCD和PBC-GEBF-VCD方法有望成为研究溶液中分子晶体和大分子手性的实用工具。

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引用次数: 1

Mapping charge-transfer excitations in Bacteriochlorophyll dimers from first principles 从第一性原理映射细菌叶绿素二聚体的电荷转移激发

IF 2.6 Q2 Physics and Astronomy

Electronic Structure

Pub Date : 2023-01-09 DOI: 10.1088/2516-1075/acd28e

Z. Hashemi, Matthias Knodt, Mário R. G. Marques, L. Leppert

Photoinduced charge-transfer excitations are key to understand the primary processes of natural photosynthesis and for designing photovoltaic and photocatalytic devices. In this paper, we use Bacteriochlorophyll dimers extracted from the light harvesting apparatus and reaction center of a photosynthetic purple bacterium as model systems to study such excitations using first-principles numerical simulation methods. We distinguish four different regimes of intermolecular coupling, ranging from very weakly coupled to strongly coupled, and identify the factors that determine the energy and character of charge-transfer excitations in each case. We also construct an artificial dimer to systematically study the effects of intermolecular distance and orientation on charge-transfer excitations, as well as the impact of molecular vibrations on these excitations. Our results provide design rules for tailoring charge-transfer excitations in Bacteriochloropylls and related photoactive molecules, and highlight the importance of including charge-transfer excitations in accurate models of the excited-state structure and dynamics of Bacteriochlorophyll aggregates.

光诱导电荷转移激发是理解自然光合作用的主要过程以及设计光伏和光催化器件的关键。在本文中，我们使用从光合紫色细菌的光采集装置和反应中心提取的细菌叶绿素二聚体作为模型系统，使用第一性原理数值模拟方法来研究这种激发。我们区分了四种不同的分子间耦合机制，从极弱耦合到强耦合，并确定了在每种情况下决定电荷转移激发的能量和特性的因素。我们还构建了一个人工二聚体，系统地研究了分子间距离和取向对电荷转移激发的影响，以及分子振动对这些激发的影响。我们的结果为定制细菌叶绿素和相关光活性分子中的电荷转移激发提供了设计规则，并强调了在细菌叶绿素聚集体的激发态结构和动力学的精确模型中包括电荷转移激发的重要性。

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引用次数: 0

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