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Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides 通过淀粉样蛋白和非淀粉样蛋白六肽导航均匀图路径
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-10-03 DOI: 10.1002/jcc.70238
László Keresztes, Evelin Szögi, Bálint Varga, Viktor Farkas, András Perczel, Vince Grolmusz

Hexapeptides are increasingly applied as model systems for studying the amyloidogenic properties of oligo- and polypeptides. It is possible to construct 64 million different hexapeptides from the twenty proteinogenic amino acid residues. Today's experimental amyloid databases contain only a fraction of these annotated hexapeptides. For labeling all the possible hexapeptides as “amyloidogenic” or “non-amyloidogenic” there exist several computational predictors with good accuracy. It may be of interest to define and study a simple graph structure on the 64 million hexapeptides as nodes, when two hexapeptides are connected by an edge if they differ by only a single residue. For example, in this graph, HIKKLM is connected to AIKKLM, or HIKKNM, or HIKKLC, but it is not connected with an edge to VVKKLM or HIKNPM. In the present contribution, we consider our previously published artificial intelligence-based tool, the Budapest Amyloid Predictor (BAP for short), and demonstrate a spectacular property of this predictor in the graph defined above. We show that for any two hexapeptides predicted to be “amyloidogenic” by the BAP predictor, there exists an easily constructible path of length at most six that passes through neighboring hexapeptides all predicted to be “amyloidogenic” by BAP. For example, the predicted amyloidogenic ILVWIW and FWLCYL hexapeptides can be connected through the length-6 path ILVWIW-IWVWIW-IWVCIW-IWVCIL-FWVCIL-FWLCIL-FWLCYL in such a way that the neighbors differ in exactly one residue, and all hexapeptides on the path are predicted to be amyloidogenic by BAP. The symmetric statement also holds true for non-amyloidogenic predicted hexapeptides: For any such pair, there exists a path of length at most six, traversing only predicted non-amyloidogenic hexapeptides. It is noted that the mentioned property of the Budapest Amyloid Predictor https://pitgroup.org/bap is not proprietary; it is also true for any linear Support Vector Machine (SVM)-based predictors; therefore, for any future improvements of BAP using the linear SVM prediction technique.

六肽越来越多地被用作研究寡肽和多肽淀粉样蛋白形成特性的模型系统。从20个蛋白质原氨基酸残基中可以构建6400万个不同的六肽。今天的实验性淀粉样蛋白数据库只包含这些注释六肽的一小部分。为了将所有可能的六肽标记为“淀粉样蛋白”或“非淀粉样蛋白”,存在几种具有良好准确性的计算预测方法。当两个六肽仅相差一个残基时,在6400万个六肽作为节点上定义和研究一个简单的图结构可能会引起人们的兴趣。例如,在这个图中,HIKKLM连接到AIKKLM,或HIKKNM,或HIKKLC,但它没有连接到VVKKLM或HIKNPM的边。在目前的贡献中,我们考虑了我们之前发表的基于人工智能的工具,布达佩斯淀粉样蛋白预测器(简称BAP),并在上面定义的图表中展示了该预测器的惊人特性。我们发现,对于被BAP预测为“淀粉样蛋白”的任意两个六肽,存在一条长度最多为6的易于构建的路径,该路径穿过被BAP预测为“淀粉样蛋白”的相邻六肽。例如,预测的致淀粉性ILVWIW和FWLCYL六肽可以通过长度为6的路径ILVWIW- iwvwiw - iwvciw - iwvcil - fwvcil - fwlcil -FWLCYL连接,使得相邻的残基恰好相差一个残基,并且该路径上的所有六肽都被BAP预测为致淀粉性。对于非淀粉样蛋白生成的预测六肽,对称陈述也成立:对于任何这样的对,存在长度最多为6的路径,只遍历预测的非淀粉样蛋白生成的六肽。值得注意的是,布达佩斯淀粉样蛋白预测器https://pitgroup.org/bap的上述特性不是专有的;对于任何基于线性支持向量机(SVM)的预测器也是如此;因此,对于未来使用线性支持向量机预测技术对BAP进行改进。
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引用次数: 0
Correction to “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D” 对“探索无铅ca3bicl3基钙钛矿太阳能电池:DFT和SCAPS-1D电荷传输层的计算比较”的更正。
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-29 DOI: 10.1002/jcc.70247

Biswas, B. C., Shimul, A. I., Ghosh, A., Awaad, N. S., and Ibrahium, H. A., “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D,” Journal of Computational Chemistry 46 (2025): e70231, https://doi.org/10.1002/jcc.70231.

The acknowledgment section has been changed as below:

The authors extend their appreciation to the Deanship of Research and Graduate Studies at King Khalid University for funding this work through Large Research Project under grant number RGP2/338/46.

We apologize for this error.

Biswas, b.c, Shimul, a.i, Ghosh, A., Awaad, N. S.和Ibrahium, H. A.,“探索无铅ca3bicl3 -钙钛矿太阳能电池:基于DFT和SCAPS-1D的电荷传输层的计算比较”,计算化学杂志46 (2025):e70231, https://doi.org/10.1002/jcc.70231.The致谢部分更改如下:作者感谢哈立德国王大学研究与研究生院院长通过大型研究项目资助本工作,资助号为RGP2/338/46。我们为这个错误道歉。
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引用次数: 0
Accurate and Cost-Efficient DLPNO-CCSD(T)-Based Feller-Peterson-Dixon Protocols Calibrated on Association Reactions of Li+ Ion With Mixed Organic Carbonates 基于DLPNO - CCSD(T) - Based的Li+离子与混合有机碳酸盐缔合反应校准的Feller - Peterson - Dixon方案准确且具有成本效益
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-29 DOI: 10.1002/jcc.70244
Arseniy A. Otlyotov, Andrey D. Moshchenkov, Alexander S. Ryzhako, Luigi Cavallo, Yury Minenkov

We present a benchmark set LIMIXCARB_RE12 comprising 12 reference DLPNO-CCSD(T1)/CPS(6,7)/CBS(cc-pwCVTZ/cc-pwCVQZ)//PBE0-D3(BJ)/def2-TZVP binding energies for the sizeable (up to 69 atoms) clusters of Li+ ion with mixed cyclic and linear organic carbonates. A number of computationally cheaper DLPNO-CCSD(T)-based Feller-Peterson-Dixon protocols including contributions due to core-valence electron correlation, using more accurate iterative triples correction (T1) and tighter-than-default PNO settings are examined with respect to their accuracy and efficiency. Particular splittings of the total binding energy into components allow maintaining high accuracy (deviations less than 0.2 kcal mol−1) at significantly reduced computational cost. Much faster convergence of the DLPNO-CCSD(T) binding energies to the reference values is reached if Ahlrichs' def2 basis sets are used instead of their correlation-consistent Dunning counterparts. Evaluation of the DFT approximations against the LIMIXCARB_RE12 reveals double hybrid PWPB95-D4 in conjunction with CBS(def2-TZVPP/def2-QZVPP) extrapolation to be the best performer with mean signed deviation (MSD) of only −0.1 kcal mol−1 followed by r2SCAN-D4/D3(BJ) and r2SCAN-3c (MSD < 1 kcal mol−1), while hybrid B3LYP and PBE0 functionals complemented with D3(BJ) or D4 dispersion corrections are clearly inferior. The obtained results provide a guide for the accurate calculations of the binding energies of the microsolvated clusters and can be used for the development and validation of the emerging computational methods.

我们提出了一个基准集LIMIXCARB_RE12,包含12个参考DLPNO‐CCSD(T1)/CPS(6,7)/CBS(cc‐pwCVTZ/cc‐pwCVQZ)//PBE0‐D3(BJ)/def2‐TZVP结合能,用于Li+离子与混合环状和线性有机碳酸盐的相当大(多达69个原子)簇。许多计算成本更低的基于DLPNO - CCSD(T)的Feller - Peterson - Dixon方案,包括由于核心价电子相关的贡献,使用更精确的迭代三重校正(T1)和比默认更严格的PNO设置,研究了它们的准确性和效率。将总结合能拆分为多个组分,可以在显著降低计算成本的情况下保持高精度(偏差小于0.2千卡摩尔−1)。如果使用Ahlrichs的def2基集而不是它们的Dunning对应基集,则可以更快地收敛DLPNO - CCSD(T)结合能到参考值。针对LIMIXCARB_RE12的DFT近似评估显示,结合CBS(def2‐TZVPP/def2‐QZVPP)外推的双杂交PWPB95‐D4表现最佳,平均符号偏差(MSD)仅为−0.1 kcal mol−1,其次是r2SCAN‐D4/D3(BJ)和r2SCAN‐3c (MSD < 1 kcal mol−1),而混合B3LYP和PBE0泛函补充D3(BJ)或D4色散校正明显较差。所得结果为微溶剂化团簇结合能的精确计算提供了指导,并可用于新兴计算方法的开发和验证。
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引用次数: 0
Quantification of Reaction Barriers Under Diffusion Controlled Conditions 扩散控制条件下反应势垒的定量
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-27 DOI: 10.1002/jcc.70233
Martin M. Maehr, Radu A. Talmazan, Maren Podewitz

In quantum chemistry, diffusion-controlled reactions are typically characterized by a monotonous rise in the electronic energy, indicative of a barrierless process. In reality, this change in electronic energy is accompanied by an increase in entropy, thereby introducing a barrier in free energy. Standard quantum-chemical models fall short in capturing this phenomenon, but we have developed a cost-efficient method to address this challenge. By tracking changes in bonding based on quantum chemical descriptors, we can model the onset of entropy along the reaction path by defining a cutoff that indicates the halfway point in the entropy gain. Utilizing a sigmoid fit function to model the entropy change, we obtain a transition state on the free energy surface for diffusion-controlled reactions. Our methodology is robust and suitable for diverse complexes within both organic and inorganic chemistry.

在量子化学中,扩散控制反应的典型特征是电子能量的单调上升,表明这是一个无障碍的过程。实际上,这种电子能量的变化伴随着熵的增加,从而在自由能中引入了一个势垒。标准的量子化学模型无法捕捉到这种现象,但我们已经开发出一种经济有效的方法来解决这一挑战。通过基于量子化学描述符跟踪成键的变化,我们可以通过定义一个表示熵增益中点的截止点来沿着反应路径模拟熵的开始。利用s型拟合函数对熵变进行建模,得到了扩散控制反应在自由能面上的过渡态。我们的方法是稳健的,适用于有机和无机化学中的各种配合物。
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引用次数: 0
Computational Exploration of Small Hydrocarbon Networks: A Stochastic Generation and DFT Refinement Framework 小碳氢化合物网络的计算探索:随机生成和DFT改进框架
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-27 DOI: 10.1002/jcc.70236
Sandip Giri, Sayon Satpati, Tarun Roy, Subhas Ghosal, Anakuthil Anoop

Small hydrocarbons are central to astrochemistry due to their prevalence and chemical reactivity across diverse interstellar environments. Here, we present HydroMol, an open-access computational platform designed for systematic exploration and analysis of hydrocarbon chemical spaces, featuring over 2700 neutral CnHm(n,m=110)$$ {mathrm{C}}_n{mathrm{H}}_mleft(n,m=1-10right) $$ hydrocarbon structures generated stochastically and refined via density functional theory at B3LYP-D3BJ/def2-SVP level. HydroMol provides detailed molecular geometries, thermodynamic parameters, and electronic properties critical for interpreting astrochemical phenomena and identifying promising observational targets. Our database, hosted within a lightweight client-side web application for rapid search and visualization, introduces approximately 2000 previously unreported hydrocarbons absent in major chemical repositories such as PubChem. Statistical analysis highlights the predominance of structurally simple monocyclic and bicyclic species, characterized by HOMO and LUMO energies centered at approximately 6$$ -6 $$ and 2$$ -2 $$ eV, respectively, and typical HOMO–LUMO gaps around 4–5 eV. The methodology is readily extendable to heavier elements and expanded property datasets, providing a valuable resource for astrochemical modeling, molecular spectroscopy, and computational hydrocarbon discovery. The HydroMol web application is freely accessible at https://hydromol.github.io.

由于小碳氢化合物在不同星际环境中的普遍存在和化学反应性,它们是天体化学的核心。在这里,我们展示了HydroMol,一个开放获取的计算平台,旨在系统地勘探和分析碳氢化合物的化学空间,具有超过2700个中性C n H m (n),m = 1−10)$$ {mathrm{C}}_n{mathrm{H}}_mleft(n,m=1-10right) $$随机生成的碳氢化合物结构,并通过密度泛函理论在b3lypp - d3bj /def2-SVP水平上进行细化。HydroMol提供了详细的分子几何形状、热力学参数和电子性质,这对解释天体化学现象和确定有希望的观测目标至关重要。我们的数据库托管在一个轻量级的客户端web应用程序中,用于快速搜索和可视化,介绍了大约2000种以前未报告的碳氢化合物,这些碳氢化合物在PubChem等主要化学存储库中是不存在的。统计分析表明,结构简单的单环和双环物质占主导地位,其特征是HOMO和LUMO能量中心分别约为- 6 $$ -6 $$和- 2 $$ -2 $$ eV,典型的HOMO - LUMO间隙约为4-5 eV。该方法很容易扩展到更重的元素和扩展的属性数据集,为天体化学建模、分子光谱和计算碳氢化合物发现提供了宝贵的资源。HydroMol web应用程序可以在https://hydromol.github.io上免费访问。
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引用次数: 0
Origin-Dependence of Dipole Moments of Charged Proteins: Theoretical Foundations and Implications, Revisited 带电蛋白偶极矩的起源依赖:理论基础和意义,再访
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-25 DOI: 10.1002/jcc.70207
Islam K. Matar, Chérif F. Matta

Electric dipole moments are widely employed in structural biology and computational chemistry as global descriptors of macromolecular charge distribution, contributing to the understanding of protein interactions, solvation, and orientation in external fields. However, for systems bearing a nonzero net charge, the dipole moment becomes explicitly dependent on the choice of coordinates origin, a consequence grounded in classical electrostatics and sometimes overlooked in structural analyses. This origin-dependence is particularly relevant in biological systems, as proteins are typically charged at physiological pH which differs from their isoelectric points (pI's). Moreover, coordinate manipulations such as centering and alignment are routinely performed during molecular dynamics simulations, docking, and structural comparisons, potentially altering the calculated dipole moment of charged systems. This study reviews the theory of the changes in the dipole moment of charged macromolecules accompanying displacements of the origin of the coordinates system. The theory is illustrated by numerical examples on representative proteins. Using the classical expression μ=μ-Qa$$ {overrightarrow{mu}}^{prime }=overrightarrow{mu}hbox{-} Qoverrightarrow{a} $$, we demonstrate that displacements of the order of a protein's radius of gyration or larger can induce dipoles several hundreds to thousands of debyes. We examine this effect across a range of proteins with varying sizes and identify trends correlating the extent of origin-induced changes with molecular size. These examples highlight the need for standardization in defining coordinate systems in dipole-related analyses. The quantum mechanical status of the dipole moment operator is discussed clarifying that only neutral systems satisfy Dirac's criteria for a true “observable”. Altogether, theory, numerical benchmarks, practical guidelines, and pedagogical insights are presented for reliably calculating and interpreting dipole moments of charged biological macromolecules.

电偶极矩被广泛应用于结构生物学和计算化学中,作为大分子电荷分布的全局描述,有助于理解蛋白质的相互作用、溶剂化和外场取向。然而,对于带有非零净电荷的系统,偶极矩变得明确地依赖于坐标原点的选择,这是基于经典静电学的结果,有时在结构分析中被忽视。这种起源依赖性在生物系统中尤为重要,因为蛋白质通常在与其等电点(pI)不同的生理pH值下带电。此外,在分子动力学模拟、对接和结构比较中,通常会进行定心和对准等坐标操作,这可能会改变带电体系的偶极矩计算结果。本文综述了带电大分子偶极矩随坐标系原点位移变化的理论。通过典型蛋白质的数值算例说明了该理论。利用经典表达式μ→' =μ→-Q∑a→$$ {overrightarrow{mu}}^{prime }=overrightarrow{mu}hbox{-} Qoverrightarrow{a} $$,我们证明了蛋白质的旋转半径量级或更大的位移可以引起几百到几千个德比的偶极子。我们在一系列不同大小的蛋白质中研究了这种效应,并确定了起源诱导的变化程度与分子大小相关的趋势。这些例子突出了在偶极子相关分析中定义坐标系统时需要标准化。讨论了偶极矩算符的量子力学状态,阐明了只有中性系统才满足真正“可观测”的狄拉克标准。总之,理论,数值基准,实践指南,和教学的见解提出了可靠的计算和解释带电生物大分子的偶极矩。
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引用次数: 0
Acetylene-Linked Phenalenyl Oligomers as a Creative Source of Extended Polyradical Character 乙炔连接的苯烯基低聚物作为扩展多自由基特性的创新来源
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-24 DOI: 10.1002/jcc.70240
Jhonatas R. Carvalho, Reed Nieman, Adelia J. A. Aquino, Dana Nachtigallová, Hans Lischka

Phenalenyl is known for its highly delocalized radical structure, making it a fundamental building block in the construction of polyradical compounds. This study explores how different connection topologies between phenalenyl units via acetylenic bridges modulate the polyradical character, as well as the electronic and magnetic properties of the resulting systems. The connection type depends on the atom occupation pattern of the phenalenyl singly occupied orbital (SOMO). Three types of connections are defined that induce different π conjugation strength. Linear di- and tetra-phenalenyl chains and cyclic tri- and tetra-phenalenyl aggregates have been investigated. High-level multireference averaged coupled cluster (MR-AQCC) calculations were performed to describe the electronic structures of these compounds. The polyradical character of the oligomers is assessed using descriptors such as singlet-triplet splitting, effectively unpaired electrons (NU). Additionally, the harmonic oscillator model of aromaticity (HOMA), multicenter index (MCI), fluctuation index (FLU), nucleus-independent chemical shifts (NICS (1)), and the anisotropy of the current-induced density (ACID) analysis are employed to characterize the influence of the phenalenyl linkages on aromaticity. Results indicate that bridges enabling stronger interaction between the SOMOs of phenalenyl units lead to a reduction in polyradical character. Aromaticity analysis corroborates these findings, revealing decreased aromaticity in rings where electron interaction occurs through the bridge. On the contrary, choosing bridging types of weak interaction leads to strong open shell character providing candidates for molecular magnetism. A comparison with the predictions of Ovchinnikov's rule is carried out both to rationalize the outcomes of the quantum chemical calculations and to highlight limitations of the rule, particularly in the treatment of quasi-degenerate states.

Phenalenyl以其高度离域的自由基结构而闻名,使其成为构建多自由基化合物的基本组成部分。本研究探讨了苯烯基单元之间通过乙炔桥的不同连接拓扑如何调节多自由基特性,以及由此产生的系统的电子和磁性能。连接类型取决于苯烯基单占据轨道(SOMO)的原子占据模式。定义了三种类型的连接,产生不同的π共轭强度。线性二苯乙烯和四苯乙烯链以及环状三苯乙烯和四苯乙烯聚集体已被研究。采用高水平多参考平均耦合簇(MR-AQCC)计算来描述这些化合物的电子结构。利用单重态-三重态分裂、有效未配对电子(NU)等描述符来评估低聚物的多自由基特征。此外,采用芳香性谐振子模型(HOMA)、多中心指数(MCI)、波动指数(FLU)、核无关化学位移(NICS(1))和电流诱导密度各向异性(ACID)分析表征了苯烯基键对芳香性的影响。结果表明,桥使更强的相互作用之间的somo的苯烯基单位导致减少多自由基的性质。芳香性分析证实了这些发现,揭示了在电子通过桥发生相互作用的环中芳香性降低。相反,选择弱相互作用的桥接类型导致了强的开壳性质,为分子磁性提供了候选者。与奥夫钦尼科夫规则的预测进行了比较,以使量子化学计算的结果合理化,并突出该规则的局限性,特别是在处理准简并态方面。
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引用次数: 0
K2AlInZ6 (Z = F, Cl, Br) Double Perovskites: Potential Candidates for Optoelectronic and Photovoltaic Devices K2AlInZ6 (Z = F, Cl, Br)双钙钛矿:光电和光伏器件的潜在候选材料。
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-23 DOI: 10.1002/jcc.70222
Samah Saidi, Soufyane Belhachi, Sahar Abdalla, Jehan Y. Al-Humaidi, M. W. Iqbal, Muneera S. M. Al-Saleem, Mohammed M. Rahman, Mika Sillanpää, Aravind Kumar, Subhav Singh

In this research, K2AlInZ6 (Z = F, Cl, Br) are double perovskite compounds with unique and complementary characteristics, rendering them exceptionally appropriate for many modern technological applications. This paper provides a thorough examination of the structural, electronic, elastic, mechanical, optical, and thermodynamic features of K2AlInZ6 (Z = F, Cl, Br) double perovskites by first-principles calculations based on density functional theory (DFT). The structural characteristics, encompassing lattice parameters and formation energies, validate the stability of these materials, which exhibit a cubic configuration with the Fm-3m space group. The electronic band structure calculations with the modified Becke-Johnson exchange potential indicate indirect band gaps for K2AlInZ6 (Z = F, Cl, Br), with band gaps of 3.73, 2.88, and 2.41 eV for K2AlInF6, K2AlInCl6, and K2AlInBr6, respectively, rendering them viable candidates for optoelectronic applications. The estimated elastic constants, bulk modulus, and shear modulus demonstrate mechanical stability, indicating their suitability for durable and flexible devices. The optical characteristics, including dielectric functions and absorption spectra, exhibit considerable absorption in the ultraviolet range, indicating their potential use in photovoltaic systems. Furthermore, the thermodynamic characteristics are examined by assessing formation energy and Debye temperature. The negative formation energies of these materials signify their strong thermodynamic stability, whereas the Debye temperature analysis elucidates their lattice vibrations and heat capacity, further substantiating their stability and applicability in diverse energy technologies. At 800 K, K2AlInF6, K2AlInCl6, and K2AlInBr6 show Seebeck coefficients of ~150, ~160, and ~135 μV/K, respectively, with κe/τ rising to ~4.0–4.75 × 1014 W/mKs. ZT values peak at ~0.69, ~0.68, and ~0.58, indicating strong thermoelectric potential at high temperatures.

在这项研究中,K2AlInZ6 (Z = F, Cl, Br)是双钙钛矿化合物,具有独特和互补的特性,使其非常适合许多现代技术应用。本文通过基于密度泛函理论(DFT)的第一性原理计算,对K2AlInZ6 (Z = F, Cl, Br)双钙钛矿的结构、电子、弹性、机械、光学和热力学特征进行了全面的研究。包括晶格参数和形成能在内的结构特征验证了这些材料的稳定性,它们呈现出具有Fm-3m空间群的立方构型。利用改进的Becke-Johnson交换电位进行电子能带结构计算表明,K2AlInZ6 (Z = F, Cl, Br)具有间接带隙,K2AlInF6、K2AlInCl6和K2AlInBr6的带隙分别为3.73、2.88和2.41 eV,这使得它们成为光电应用的可行候选材料。估计的弹性常数、体积模量和剪切模量显示出机械稳定性,表明它们适用于耐用和柔性的设备。光学特性,包括介电函数和吸收光谱,在紫外范围内表现出相当大的吸收,表明它们在光伏系统中的潜在应用。此外,通过评估地层能量和德拜温度来检查热力学特性。这些材料的负形成能表明它们具有很强的热力学稳定性,而Debye温度分析阐明了它们的晶格振动和热容量,进一步证实了它们的稳定性和在各种能源技术中的适用性。在800 K时,K2AlInF6、K2AlInCl6和K2AlInBr6的Seebeck系数分别为~150、~160和~135 μV/K, κe/τ为~4.0 ~ 4.75 × 1014 W/ mk。ZT值在~0.69、~0.68和~0.58处达到峰值,表明高温下热电势强。
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引用次数: 0
Stability and Reactivity of TiO 2 n $$ {left({mathrm{TiO}}_2right)}_n $$ , n = 1–10, Clusters and Their Interactions With CO 2 $$ {mathrm{CO}}_2 $$ tio2 (n = 1-10)簇的稳定性和反应性及其与CO2的相互作用
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-20 DOI: 10.1002/jcc.70232
Letícia Carolaine Silva Faria, Letícia Marques de Souza Vetrano de Queiroz, Murielly Fernanda Ribeiro Bihain, Douglas Henrique Pereira, Leonardo Tsuyoshi Ueno, Francisco Bolivar Correto Machado, Luiz Fernando de Araujo Ferrão
<p>Small titanium dioxide clusters <span></span><math> <semantics> <mrow> <msub> <mfenced> <msub> <mi>TiO</mi> <mn>2</mn> </msub> </mfenced> <mi>n</mi> </msub> </mrow> <annotation>$$ {left({mathrm{TiO}}_2right)}_n $$</annotation> </semantics></math> (with <span></span><math> <semantics> <mrow> <mi>n</mi> </mrow> <annotation>$$ n $$</annotation> </semantics></math> = 1–10) are promising photocatalysts for <span></span><math> <semantics> <mrow> <msub> <mi>CO</mi> <mn>2</mn> </msub> </mrow> <annotation>$$ {mathrm{CO}}_2 $$</annotation> </semantics></math> conversion; however, their size-dependent stability and reactivity are not fully characterized. This study uses density functional theory (M06/def2-TZVP) and global and local reactivity descriptors to identify “magic number” clusters that exhibit high stability. The stability function (<span></span><math> <semantics> <mrow> <msup> <mi>ε</mi> <mn>3</mn> </msup> </mrow> <annotation>$$ {varepsilon}^3 $$</annotation> </semantics></math>), reveals <span></span><math> <semantics> <mrow> <mi>n</mi> </mrow> <annotation>$$ n $$</annotation> </semantics></math> = 2, 4, and 8 as magic numbers. Electrophilicity analysis (<span></span><math> <semantics> <mrow> <mi>Δ</mi> <mi>ω</mi> </mrow> <annotation>$$ Delta omega $$</annotation> </semantics></math>) shows moderate electrophilicity for <span></span><math> <semantics> <mrow> <mi>n</mi> </mrow> <annotation>$$ n $$</annotation> </semantics></math> = 1–5 and strong electrophilicity for <span></span><math> <semantics> <mrow> <mi>n</mi> </mrow> <annotation>$$ n $$</annotation> </semantics></math> = 7–10, while the magic numbers display reduced reactivity. Fukui functions and fractional occupation number-weighted density (<span></span><math> <semantics>
小的二氧化钛团簇(TiO2)n $$ {left({mathrm{TiO}}_2right)}_n $$ (n $$ n $$ = 1-10)是很有前途的CO2 $$ {mathrm{CO}}_2 $$转化光催化剂;然而,它们的尺寸依赖性稳定性和反应性尚未完全表征。本研究使用密度泛函理论(M06/def2-TZVP)和全局和局部反应性描述符来识别具有高稳定性的“幻数”簇。稳定性函数(ε3 $$ {varepsilon}^3 $$)显示n $$ n $$ = 2,4和8为幻数。亲电性分析(Δ¹ω $$ Delta omega $$)表明,n $$ n $$ = 1-5时亲电性中等,n $$ n $$ = 7-10时亲电性强,而魔术数显示反应性降低。福井函数和分数职业数加权密度(NFOD $$ {N}_{FOD} $$)强调局部反应性。值得注意的是,它们显示n $$ n $$ = 6具有高度亲电性,具有明显的“热”电子位。CO2 $$ {mathrm{CO}}_2 $$相互作用能量与团簇稳定性呈负相关:不稳定的团簇(n $$ n $$ = 3,5和9)强烈地结合CO2 $$ {mathrm{CO}}_2 $$(高达0.72 eV),而幻数则弱地物理吸收它(例如,n $$ n $$ = 8时,0.45 eV)。非共价相互作用(NCI)分析证实了Ti-OCO吸引位点和c -排斥位点。总之,这些结果建立了TiO2 $$ {mathrm{TiO}}_2 $$团簇催化剂的设计原则,平衡了CO2 $$ {mathrm{CO}}_2 $$活化的稳定性和定制反应性。
{"title":"Stability and Reactivity of \u0000 \u0000 \u0000 \u0000 \u0000 \u0000 TiO\u0000 2\u0000 \u0000 \u0000 n\u0000 \u0000 \u0000 $$ {left({mathrm{TiO}}_2right)}_n $$\u0000 , n = 1–10, Clusters and Their Interactions With \u0000 \u0000 \u0000 \u0000 CO\u0000 2\u0000 \u0000 \u0000 $$ {mathrm{CO}}_2 $$","authors":"Letícia Carolaine Silva Faria,&nbsp;Letícia Marques de Souza Vetrano de Queiroz,&nbsp;Murielly Fernanda Ribeiro Bihain,&nbsp;Douglas Henrique Pereira,&nbsp;Leonardo Tsuyoshi Ueno,&nbsp;Francisco Bolivar Correto Machado,&nbsp;Luiz Fernando de Araujo Ferrão","doi":"10.1002/jcc.70232","DOIUrl":"10.1002/jcc.70232","url":null,"abstract":"&lt;p&gt;Small titanium dioxide clusters &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;TiO&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {left({mathrm{TiO}}_2right)}_n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; (with &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; = 1–10) are promising photocatalysts for &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;CO&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{CO}}_2 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; conversion; however, their size-dependent stability and reactivity are not fully characterized. This study uses density functional theory (M06/def2-TZVP) and global and local reactivity descriptors to identify “magic number” clusters that exhibit high stability. The stability function (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mi&gt;ε&lt;/mi&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {varepsilon}^3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;), reveals &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; = 2, 4, and 8 as magic numbers. Electrophilicity analysis (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;Δ&lt;/mi&gt;\u0000 &lt;mi&gt;ω&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Delta omega $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) shows moderate electrophilicity for &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; = 1–5 and strong electrophilicity for &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; = 7–10, while the magic numbers display reduced reactivity. Fukui functions and fractional occupation number-weighted density (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Leveraging the Bias-Variance Tradeoff in Quantum Chemistry for Accurate Negative Singlet-Triplet Gap Predictions: A Case for Double-Hybrid DFT 利用量子化学中的偏差-方差权衡来准确预测负单重态-三重态间隙:双杂化DFT的一个案例。
IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-09-18 DOI: 10.1002/jcc.70228
Atreyee Majumdar, Raghunathan Ramakrishnan
<p>Molecules that have been suggested to violate the Hund's rule, having a first excited singlet state (<span></span><math> <semantics> <mrow> <msub> <mrow> <mtext>S</mtext> </mrow> <mrow> <mn>1</mn> </mrow> </msub> </mrow> <annotation>$$ {mathrm{S}}_1 $$</annotation> </semantics></math>) energetically below the triplet state (<span></span><math> <semantics> <mrow> <msub> <mrow> <mtext>T</mtext> </mrow> <mrow> <mn>1</mn> </mrow> </msub> </mrow> <annotation>$$ {mathrm{T}}_1 $$</annotation> </semantics></math>), are rare. Yet, they hold the promise to be efficient light emitters. Their high-throughput identification demands exceptionally accurate excited-state modeling to minimize qualitatively wrong predictions. We benchmark twelve <span></span><math> <semantics> <mrow> <msub> <mrow> <mtext>S</mtext> </mrow> <mrow> <mn>1</mn> </mrow> </msub> <mo>−</mo> <msub> <mrow> <mtext>T</mtext> </mrow> <mrow> <mn>1</mn> </mrow> </msub> </mrow> <annotation>$$ {mathrm{S}}_1-{mathrm{T}}_1 $$</annotation> </semantics></math> energy gaps to find that the local-correlated versions of ADC(2) and CC2 excited state methods deliver excellent accuracy and speed for screening medium-sized molecules. Notably, we find that double-hybrid DFT approximations (e.g., B2GP-PLYP and PBE-QIDH) exhibit high mean absolute errors (<span></span><math> <semantics> <mrow> <mo>></mo> <mn>100</mn> <mspace></mspace> <mtext>meV</mtext> </mrow> <annotation>$$ >100kern0.3em mathrm{meV} $$</annotation> </semantics></math>) despite very low standard deviations (<span></span><math> <semantics> <mrow> <mo>≈</mo> <mn>10</mn> <mspace></mspace> <mtext>meV</mtext> </mrow>
被认为违反洪德定律的分子,在能量上低于三重态(t1 $$ {mathrm{T}}_1 $$)的第一激发态(s1 $$ {mathrm{S}}_1 $$)是非常罕见的。然而,它们有望成为高效的发光体。它们的高通量识别要求异常精确的激发态建模,以尽量减少定性错误的预测。我们对12个s1 - t1 $$ {mathrm{S}}_1-{mathrm{T}}_1 $$能隙进行了基准测试,发现ADC(2)和CC2激发态方法的局部相关版本为筛选中等大小的分子提供了出色的准确性和速度。值得注意的是,我们发现双混合DFT近似(例如,B2GP-PLYP和PBE-QIDH)具有很高的平均绝对误差(bbb100 meV $$ >100kern0.3em mathrm{meV} $$),尽管标准偏差非常低(≈10 meV $$ approx 10kern0.3em mathrm{meV} $$)。探索它们的参数空间揭示了一个75% exchange and 55% correlation, which reduces the mean absolute error to below 5 meV, but with an increased variance. Using this low-bias parameterization as an internal reference, we correct the systematic error while maintaining low variance, effectively combining the strengths of both low-bias and low-variance DFT parameterizations to enhance overall accuracy. Our findings suggest that low-variance DFT methods, often overlooked due to their high bias, can serve as reliable tools for predictive modeling in first-principles molecular design. The bias-correction data-fitting procedure can be applied to any general problem where two flavors of a method, one with low bias and another with low variance, have been identified a priori.
{"title":"Leveraging the Bias-Variance Tradeoff in Quantum Chemistry for Accurate Negative Singlet-Triplet Gap Predictions: A Case for Double-Hybrid DFT","authors":"Atreyee Majumdar,&nbsp;Raghunathan Ramakrishnan","doi":"10.1002/jcc.70228","DOIUrl":"10.1002/jcc.70228","url":null,"abstract":"&lt;p&gt;Molecules that have been suggested to violate the Hund's rule, having a first excited singlet state (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;S&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{S}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) energetically below the triplet state (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;T&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{T}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;), are rare. Yet, they hold the promise to be efficient light emitters. Their high-throughput identification demands exceptionally accurate excited-state modeling to minimize qualitatively wrong predictions. We benchmark twelve &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;S&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;T&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{S}}_1-{mathrm{T}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; energy gaps to find that the local-correlated versions of ADC(2) and CC2 excited state methods deliver excellent accuracy and speed for screening medium-sized molecules. Notably, we find that double-hybrid DFT approximations (e.g., B2GP-PLYP and PBE-QIDH) exhibit high mean absolute errors (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;&gt;&lt;/mo&gt;\u0000 &lt;mn&gt;100&lt;/mn&gt;\u0000 &lt;mspace&gt;&lt;/mspace&gt;\u0000 &lt;mtext&gt;meV&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ &gt;100kern0.3em mathrm{meV} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) despite very low standard deviations (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;≈&lt;/mo&gt;\u0000 &lt;mn&gt;10&lt;/mn&gt;\u0000 &lt;mspace&gt;&lt;/mspace&gt;\u0000 &lt;mtext&gt;meV&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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Journal of Computational Chemistry
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