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Reparameterized semi-empirical methods for computing anharmonic vibrational frequencies of multiply-bonded hydrocarbons 计算多键碳氢化合物非谐波振动频率的重参数化半经验方法
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-11-18 DOI: 10.1088/2516-1075/aca458
B. R. Westbrook, Joshua P Layfield, Timothy J. Lee, R. Fortenberry
Reparameterized semi-empirical methods can reproduce gas-phase experimental vibrational frequencies to within 24 cm−1 or better for a 100-fold decrease in computational cost in the anharmonic fundamental vibrational frequencies. To achieve such accuracy and efficiency, the default parameters in the PM6 semi-empirical model are herein optimized to reproduce the experimental and high-level theoretical vibrational spectra of three small hydrocarbon molecules, C2H2, c-C3H2, and C2H4, with the hope that these same parameters will be applicable to large polycyclic aromatic hydrocarbons (PAHs). This massive cost reduction allows for the computation of explicit anharmonic frequencies and the inclusion of resonance corrections that have been shown to be essential for accurate predictions of anharmonic frequencies. Such accurate predictions are necessary to help to disentangle the heretofore unidentified infrared spectral features observed around diverse astronomical bodies and hypothesized to be caused by PAHs, especially with the upcoming influx of observational data from the James Webb Space Telescope. The optimized PM6 parameters presented herein represent a substantial step in this direction with those obtained for ethylene (C2H4) yielding a 37% reduction in the mean absolute error of the fundamental frequencies compared to the default PM6 parameters.
重新参数化的半经验方法可以将气相实验振动频率复制到24 cm−1或更好的范围内,从而将非谐波基本振动频率的计算成本降低100倍。为了实现这样的准确性和效率,本文对PM6半经验模型中的默认参数进行了优化,以再现C2H2、c-C3H2和C2H4这三个小烃分子的实验和高级理论振动光谱,希望这些相同的参数将适用于大的多环芳烃(PAHs)。这种大规模的成本降低允许计算显式非谐波频率,并包括已被证明对非谐波频率的精确预测至关重要的谐振校正。这种准确的预测是必要的,有助于解开迄今为止在不同天体周围观察到的、被假设是由多环芳烃引起的未经识别的红外光谱特征,特别是随着詹姆斯·韦伯太空望远镜即将涌入的观测数据。本文提出的优化的PM6参数代表了在这个方向上的实质性步骤,对于乙烯(C2H4)获得的那些参数与默认的PM6参量相比,基频的平均绝对误差减少了37%。
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引用次数: 3
High-level quantum chemistry exploration of reduction by group-13 hydrides: insights into the rational design of bio-mimic CO2 reduction 13族氢化物还原的高级量子化学探索:对生物模拟CO2还原的合理设计的见解
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-11-07 DOI: 10.1088/2516-1075/ac9bb3
B. Chan, Masanari Kimura
In the present study, we have used computational quantum chemistry to explore the reduction of various types of substrates by group-13 hydrides. We use the high-level L-W1X method to obtain the energies for the constituent association and hydride transfer reactions. We find that the hydride transfer reactions are highly exothermic, while the preceding association reactions are less so. Thus, improving the thermodynamics of substrate association may improve the overall process. Among the various substrates, amine and imine show the strongest binding, while CO2 shows the weakest. Between the group-13 hydrides, alanes bind most strongly with the substrates, and they also have the most exothermic hydride transfer reactions. To facilitate CO2 binding, we have examined alanes with electron-withdrawing groups, and we indeed find CF3 groups to be effective. Drawing inspiration from the RuBisCO enzyme for CO2 fixation, we have further examined the activation of CO2 with two independent AlH(CF3)2 molecules, with the results showing an even more exothermic association. This observation may form the basis for designing an effective dialane reagent for CO2 reduction. We have also assessed a range of lower-cost computational methods for the calculation of systems in the present study. We find the DSD-PBEP86 double-hybrid DFT method to be the most suitable for the study of related medium-sized systems.
在本研究中,我们利用计算量子化学探索了13族氢化物对各种底物的还原作用。我们用高能级L-W1X方法得到了组份缔合反应和氢化物转移反应的能量。我们发现氢化物转移反应是高度放热的,而前面的缔合反应则不那么放热。因此,提高底物缔合的热力学可以改善整个过程。在各种底物中,胺和亚胺的结合最强,而CO2的结合最弱。在13族氢化物中,烷烃与底物结合最强烈,并且它们也有最多的放热氢化物转移反应。为了促进二氧化碳的结合,我们研究了带有吸电子基团的烷烃,我们确实发现CF3基团是有效的。受RuBisCO酶固定CO2的启发,我们进一步研究了两个独立的AlH(CF3)2分子对CO2的激活,结果显示出更大的放热关联。这一观察结果可作为设计一种有效的二烷试剂用于CO2还原的基础。在本研究中,我们还评估了一系列用于系统计算的低成本计算方法。我们发现DSD-PBEP86双混合DFT方法最适合于相关中型系统的研究。
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引用次数: 0
A unified secondary electron cut-off presentation and common mistakes in photoelectron spectroscopy 统一的二次电子截止表示及光电子能谱中的常见错误
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-11-03 DOI: 10.1088/2516-1075/ac9ffb
T. Schultz
Photoelectron spectroscopy is a powerful surface analysis technique that can differentiate different bonding environments and directly determine the absolute work function of a sample. Despite its ever-easier accessibility—or perhaps precisely because of it—some common mistakes or bad habits are often found in the literature when it comes to the evaluation or presentation of photoelectron spectroscopy data. Here we address some of these issues and give suggestions for best practice, i.e., a proper presentation of the secondary electron cut-off used for work function determination, correct binding energy referencing and some tips for appropriate peak fitting, as well as valuable literature references to more detailed tutorials. Finally, we present a concise step-by-step guide on how to conduct a complete x-ray photoelectron spectroscopy analysis of an unknown sample.
光电子能谱是一种强大的表面分析技术,可以区分不同的键合环境,并直接确定样品的绝对功函数。尽管它越来越容易获得——或者可能正是因为它——但在评估或呈现光电子能谱数据时,文献中经常会发现一些常见的错误或坏习惯。在这里,我们解决了其中的一些问题,并提出了最佳实践的建议,即,用于功函数确定的二次电子截止的正确表示、正确的结合能参考和适当峰值拟合的一些技巧,以及更详细教程的有价值的文献参考。最后,我们提供了一个关于如何对未知样品进行完整的x射线光电子能谱分析的简明分步指南。
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引用次数: 7
Non-empirical double-hybrid density functionals as reliable tools for electronic structure calculations 非经验双混合密度泛函作为电子结构计算的可靠工具
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-10-11 DOI: 10.1088/2516-1075/ac9942
J. Sancho‐García, É. Brémond, Á. Pérez‐Jiménez, Ilaria Ciofini, C. Adamo
The development of universal and accurate approximations for electronic structure calculations lies at the central core of (past and modern) research in theoretical and computational chemistry. For that purpose, any reliable method needs to treat in a balanced way exchange and correlation effects arising from the intricate structure of matter at the nanoscopic level. Following this principle, we have developed a set of non-empirical (double-hybrid) density functional expressions, minimizing the parameterization and also widely applicable even for systems of considerable size, while being accurate enough to compete with wavefunction methods or even matching experimental information. The underlying expressions are now implemented in many available codes worldwide, then allowing the access to the whole set of key properties needed for addressing chemical structure, reactivity, and bonding, at all nanostructured levels and/or states of matter. Additionally, the recent extension to excited states through a time-dependent (linear-response) formalism also allows one to deal with photochemistry, photophysical, and related properties. Therefore, this family of methods can now be successfully applied to organic, inorganic, or biomolecular compounds, or any other complex system, within an affordable computational effort.
电子结构计算的通用和精确近似的发展是理论和计算化学(过去和现代)研究的核心。为此,任何可靠的方法都需要以平衡的方式处理纳米级物质复杂结构产生的交换和关联效应。根据这一原理,我们开发了一组非经验(双混合)密度函数表达式,最大限度地减少了参数化,甚至广泛适用于相当大的系统,同时足够精确,可以与波函数方法竞争,甚至匹配实验信息。现在,在世界各地的许多可用代码中实现了基本的表达,从而允许在所有纳米结构水平和/或物质状态下获得解决化学结构、反应性和键合所需的整套关键特性。此外,最近通过时间相关(线性响应)形式对激发态的扩展也允许人们处理光化学、光物理和相关性质。因此,这一系列方法现在可以在负担得起的计算工作量内成功应用于有机、无机或生物分子化合物,或任何其他复杂系统。
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引用次数: 2
A divide-and-conquer method to improve performance in quantum transport calculations: conductance in rotated graphene nanoribbons side-contact junctions 一种提高量子输运计算性能的分而治之的方法:旋转石墨烯纳米带侧面接触结中的电导
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-09-30 DOI: 10.1088/2516-1075/ac96b8
M. J. Rodríguez, Carlos Ramírez
We propose a divide-and-conquer algorithm to find recursively the scattering matrix of general tight-binding structures. The scattering matrix allows a direct calculation of transport properties in mesoscopic systems by using the Landauer formula. The method is exact, and by analyzing the performance of the algorithm in square, triangular and honeycomb lattices, we show a significant improvement in comparison to other state-of-the-art recursive and non-recursive methods. We utilize this algorithm to compute the conductance of a rotated graphene nanoribbon side-contact junction, revealing that for electrons with energies smaller than −2.7 eV the transmission function depends negligibly on the angle of the junction, whereas for electrons with energies greater than −2.7 eV, there exists a set of angles for the system that increase its conductance independently of the energy of the particles.
我们提出了一种递推求解一般紧束缚结构散射矩阵的分治算法。散射矩阵允许使用Landauer公式直接计算介观系统中的输运性质。该方法是精确的,通过分析该算法在正方形、三角形和蜂窝格中的性能,与其他最先进的递归和非递归方法相比,我们显示出显著的改进。我们利用该算法计算了旋转石墨烯纳米带侧接触结的电导,揭示了对于能量小于-2.7eV的电子,传输函数可忽略地取决于结的角度,而对于能量大于-2.7eV的电子,系统存在一组角度,这些角度独立于粒子的能量来增加其电导。
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引用次数: 0
Diabatic potential energy surfaces and semiclassical multi-state dynamics for fourteen coupled 3 A′ states of O3 O3 14个3A′态耦合的非绝热势能面和半经典多态动力学
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-09-23 DOI: 10.1088/2516-1075/ac94ac
Z. Varga, Yinan Shu, Jiaxin Ning, D. Truhlar
Dissociation and energy transfer in high-energy collisions of O2 play important roles in simulating thermal energy content and heat flux in flows around hypersonic vehicles. Furthermore, atomic oxygen reactions on the vehicle surface are an important contributor to heat shield erosion. Molecular dynamics modeling is needed to better understand the relevant rate processes. Because it is necessary to model the gas flows in high-temperature shock waves, electronically excited states of O2 and O can be populated, and molecular dynamics simulations should include collisions of electronically excited species and electronically nonadiabatic collisions. This requires potential energy surfaces and state couplings for many energetically accessible electronic states. Here we report a systematic strategy to calculate such surfaces and couplings. We have applied this method to the fourteen lowest-energy potential energy surfaces in the 3 A′ manifold of O3, and we report a neural-network fit to diabatic potential energy matrix (DPEM). We illustrate the use of the resulting DPEM by carrying out semiclassical dynamics calculations of cross sections for excitation of O2 in 3 A′ collisions with O at two collision energies; these dynamics calculations are carried out by the curvature-driven coherent switching with decay of mixing method.
O2高能碰撞中的离解和能量传递在模拟高超音速飞行器周围流动的热能含量和热通量方面发挥着重要作用。此外,车辆表面的原子氧反应是隔热板侵蚀的重要原因。需要建立分子动力学模型来更好地理解相关的速率过程。由于有必要对高温冲击波中的气体流动进行建模,因此可以填充O2和O的电子激发态,分子动力学模拟应包括电子激发物种的碰撞和电子非绝热碰撞。这需要势能表面和许多能量可访问的电子态的状态耦合。在这里,我们报告了一个系统的策略来计算这样的表面和耦合。我们将该方法应用于O3的3A′流形中的14个最低能量势能面,并报道了一个适用于非绝热势能矩阵(DPEM)的神经网络。我们通过在两个碰撞能量下对3A'碰撞中O2与O的激发横截面进行半经典动力学计算来说明所得到的DPEM的使用;这些动力学计算是用混合衰减的曲率驱动相干开关方法进行的。
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引用次数: 5
Modified HSE06 functional applied to anatase TiO2: influence of exchange fraction on the quasiparticle electronic structure and optical response 改性HSE06官能团在锐钛矿TiO2上的应用:交换分数对准粒子电子结构和光学响应的影响
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-09-02 DOI: 10.1088/2516-1075/ac8f03
Sruthil lal S B, Murali D, M. Posselt, A. A. Sasikala Devi, A. Sharan
The influence of non-interacting Kohn–Sham Hamiltonian on the non-self consistent GW(G 0 W 0) quasiparticle gap and Bethe–Salpeter-equation (BSE) optical spectra of anatase TiO2 is systematically evaluated. G 0 W 0 and BSE calculations are carried out starting with HSE06 (Heyd–Scuseria–Ernzerhof) type functionals containing 20%, 25% and 30% exact Hartree–Fock exchange. The results are also compared against G 0 W 0 + BSE calculations starting from semi-local (PBE) functionals. Our results indicate that the G 0 W 0 and BSE calculations of anatase TiO2 depend critically on the mean-field starting point, wherein its dependence is mainly introduced through the dielectric screening evaluated at the intermediate G 0 W 0. We find that the band dispersion, density of states, and consequently the oscillator strengths of optical excitation and spatial localization of excitons are insensitive to the starting points while the quasiparticle gap, optical gap and exciton binding energies are strongly affected. G 0 W 0 quasiparticle gap of anatase TiO2 computed over hybrid functional starting points is typically overestimated compared to measured values. However, by varying the amount of exact exchange, the dielectric screening can be tuned, and thus the quasiparticle gap. Exciton binding energy is shown to increase in proportion to the increase of the amount of exact exchange. A simple extrapolation of the calculated data leads to the exact match with the recently measured value with 13% of the exact exchange. Systematic analysis of G 0 W 0 + BSE calculation starting from screened hybrid functionals provided in this study forms a reference for all such future calculations of pristine anatase TiO2 and its derivatives.
系统地评价了非相互作用的Kohn-Sham哈密顿量对锐钛矿TiO2非自一致GW(g0 w0)准粒子间隙和bethe - salpeter方程(BSE)光谱的影响。g0 w0和BSE计算从HSE06 (Heyd-Scuseria-Ernzerhof)型函数开始,包含20%,25%和30%的精确Hartree-Fock交换。结果还与从半局部(PBE)泛函开始的g0 w0 + BSE计算进行了比较。我们的研究结果表明,锐钛矿TiO2的g0w0和BSE计算严重依赖于平均场起点,其中其依赖性主要通过在中间g0w0处评估的介电筛选引入。我们发现带色散、态密度以及由此产生的光激发和激子空间局域化的振子强度对起始点不敏感,而准粒子间隙、光间隙和激子结合能则受到强烈影响。与测量值相比,在杂化功能起点上计算的锐钛矿TiO2的g0w0准颗粒间隙通常被高估。然而,通过改变精确交换的量,可以调整介电屏蔽,从而调整准粒子间隙。激子结合能随精确交换量的增加而成比例地增加。对计算出的数据进行简单的外推,可以使其与最近的测量值精确匹配,而精确交换的比例为13%。本研究提供的从筛选的杂化官能团开始的g0 w0 + BSE计算的系统分析,为未来所有原始锐钛矿TiO2及其衍生物的计算提供了参考。
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引用次数: 4
Insights into the stability of engineered mini-proteins from their dynamic electronic properties 从动态电子特性深入了解工程微型蛋白的稳定性
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-08-24 DOI: 10.1088/2516-1075/ac8c73
A. Steeves, H. Kulik
An understanding of protein stability requires capturing dynamic rearrangements and coupled properties over long lengthscales. Nevertheless, the extent of coupling in these systems has typically only been studied for classical degrees of freedom. To understand the potential benefit of extending such analysis to the coupling of electronic structure properties, we have carried out extensive semi-empirical quantum mechanical molecular dynamics of two Trp-cage variants. Small differences in the sequence of the two peptides lead to differences in their thermal stability that are revealed through electronic structure coupling analysis. In comparison, we find limited evidence that geometric coupling can distinguish the behavior of the two peptides. We show that Asp1 in the more stable variant shows significantly enhanced coupling to both sequence-adjacent and more sequence-distant residues. Non-nearest-neighbor couplings are stronger in the more stable variant, indicating a network of residues that help stabilize the protein. Our study highlights the complementary benefit of charge coupling analysis to interpret protein structure-function relationships.
对蛋白质稳定性的理解需要捕获长长度尺度上的动态重排和耦合特性。然而,这些系统的耦合程度通常只对经典自由度进行了研究。为了了解将这种分析扩展到电子结构特性耦合的潜在好处,我们对两种Trp-cage变体进行了广泛的半经验量子力学分子动力学研究。通过电子结构耦合分析,揭示了两种肽序列的微小差异导致其热稳定性的差异。相比之下,我们发现有限的证据表明几何耦合可以区分两个肽的行为。我们发现,在更稳定的变异中,Asp1与序列邻近和更远的残基的偶联性显著增强。非最近邻偶联在更稳定的变体中更强,表明残基网络有助于稳定蛋白质。我们的研究强调了电荷耦合分析在解释蛋白质结构-功能关系方面的互补优势。
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引用次数: 1
Local electron correlation effects on the fermiology of the weak itinerant ferromagnet ZrZn2 弱流动铁磁体ZrZn2发酵过程中的局域电子关联效应
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-08-23 DOI: 10.1088/2516-1075/ac9d79
Wenhan Chen, A. James, S. Dugdale
The Fermi surface topology plays an important role in the macroscopic properties of metals. It can be particularly sensitive to electron correlation, which appears to be especially significant for the weak itinerant ferromagnet ZrZn2. Here, we look at the differences in the predicted Fermi surface sheets of this metallic compound in its paramagnetic phase for both density functional theory (DFT) and the combination of DFT with dynamical mean field theory (DFT + DMFT). The theoretical spectral functions evaluated at the Fermi level were used along with calculations of the electron–positron momentum density (also known as the two-photon momentum density) in k-space to provide insights into the origin of certain features of the Fermi surface topology. We compare this two photon momentum density to that extracted from the positron annihilation experimental data (2004 Phys. Rev. Lett. 92 107003). The DFT + DMFT densities are in better agreement with the experiment than the DFT, particularly with regard to the flat bands around the L and W high symmetry points. The experimental neck around L, which relates to a van Hove singularity, is present in DFT + DMFT but not in the DFT. We find that these flat bands, and as such the Fermi surface topology, are sensitive to the many body electron correlation description, and show that the positron annihilation technique is able to probe this. This description is significant for the observed behavior such as the Lifshiftz transition around the quantum critical point.
费米表面拓扑在金属的宏观性质中起着重要的作用。它对电子相关特别敏感,这对弱流动铁磁体ZrZn2尤其明显。在这里,我们研究了密度泛函理论(DFT)和DFT与动态平均场理论(DFT + DMFT)相结合预测的金属化合物在顺磁相中的费米表面片的差异。在费米能级评估的理论谱函数与k空间中电子-正电子动量密度(也称为双光子动量密度)的计算一起使用,以提供对费米表面拓扑某些特征起源的见解。我们将这两个光子的动量密度与从正电子湮灭实验数据中提取的动量密度进行比较。Rev. Lett. 92 107003)。DFT + DMFT密度比DFT密度更符合实验结果,特别是在L和W高对称点周围的平坦带方面。与van Hove奇点有关的L周围的实验颈在DFT + DMFT中存在,但在DFT中不存在。我们发现这些平坦带和费米表面拓扑对多体电子相关描述是敏感的,并表明正电子湮灭技术能够探测到这一点。这种描述对于观测到的行为,如围绕量子临界点的Lifshiftz跃迁,是很重要的。
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引用次数: 4
Floquet formulation of the dynamical Berry-phase approach to nonlinear optics in extended systems 扩展系统中非线性光学的动态berry相位法的Floquet公式
IF 2.6 Q2 Physics and Astronomy Pub Date : 2022-08-22 DOI: 10.1088/2516-1075/acbc5e
Ignacio M. Alliati, M. Grüning
We present a Floquet scheme for the ab-initio calculation of nonlinear optical properties in extended systems. This entails a reformulation of the real-time approach based on the dynamical Berry-phase polarisation (Attaccalite and Grüning 2013 Phys. Rev. B 88 1–9) and retains the advantage of being non-perturbative in the electric field. The proposed method applies to periodically-driven Hamiltonians and makes use of this symmetry to turn a time-dependent problem into a self-consistent time-independent eigenvalue problem. We implemented this Floquet scheme at the independent particle level and compared it with the real-time approach. Our reformulation reproduces real-time-calculated 2nd and 3rd order susceptibilities for a number of bulk and two-dimensional materials, while reducing the associated computational cost by one or two orders of magnitude.
我们提出了一个Floquet格式,用于扩展系统中非线性光学性质的从头计算。这需要重新制定基于动态Berry相位极化的实时方法(Attacalite和Grüning 2013 Phys.Rev.B 88 1–9),并保留了在电场中不受扰动的优势。该方法适用于周期驱动的哈密顿量,并利用这种对称性将含时问题转化为自洽的时间无关特征值问题。我们在独立粒子级别上实现了Floquet方案,并将其与实时方法进行了比较。我们的公式再现了许多大块和二维材料的实时计算的二阶和三阶磁化率,同时将相关的计算成本降低了一到两个数量级。
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引用次数: 0
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Electronic Structure
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