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ABLRI: A program for calculating the long-range interaction energy between two monomers in their non-degenerate states ABLRI:计算两个单体在非退化状态下长程相互作用能的程序
Pub Date : 2024-05-01 DOI: 10.1063/5.0205486
Yipeng Yu, Dongzheng Yang, Xixi Hu, Daiqian Xie
An accurate description of the long-range (LR) interaction is essential for understanding the collision between cold or ultracold molecules. However, to our best knowledge, there lacks a general approach to construct the intermolecular potential energy surface (IPES) between two arbitrary molecules and/or atoms in the LR region. In this work, we derived analytical expressions of the LR interaction energy, using the multipole expansion of the electrostatic interaction Hamiltonian and the non-degenerate perturbation theory. To make these formulae practical, we also derived the independent Cartesian components of the electrostatic properties, including the multipole moments and polarizabilities, of the monomer for a given symmetry using the properties of these components and the group-theoretical methods. Based on these newly derived formulae, we developed a FORTRAN program, namely ABLRI, which is capable of calculating the interaction energy between two arbitrary monomers both in their non-degenerate electronic ground states at large separations. To test the reliability of this newly developed program, we constructed IPESs for the electronic ground state of H2O–H2 and O2–H systems in the LR region. The interaction energy computed by our program agreed well with the ab initio calculation, which shows the validity of this program.
准确描述长程(LR)相互作用对于理解冷分子或超冷分子之间的碰撞至关重要。然而,据我们所知,目前还缺乏一种通用方法来构建两个任意分子和/或原子之间在长程作用区域的分子间势能面(IPES)。在这项工作中,我们利用静电相互作用哈密顿的多极扩展和非退化扰动理论,推导出了 LR 相互作用能的分析表达式。为了使这些公式实用化,我们还利用这些分量的性质和群论方法,推导出了给定对称性下单体静电性质的独立笛卡尔分量,包括多极矩和极化率。根据这些新推导出的公式,我们开发了一个 FORTRAN 程序,即 ABLRI,该程序能够计算两个任意单体在大间隔非退化电子基态下的相互作用能。为了测试这一新开发程序的可靠性,我们构建了 H2O-H2 和 O2-H 系统在 LR 区域的电子基态 IPES。我们的程序计算出的相互作用能与 ab initio 计算结果非常吻合,这表明了该程序的有效性。
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引用次数: 0
Rate theory of gas–liquid nucleation: Quest for the elusive quantitative accuracy 气液成核的速率理论:追求难以捉摸的定量准确性
Pub Date : 2024-05-01 DOI: 10.1063/5.0202884
Subhajit Acharya, Biman Bagchi
The task of a first principles theoretical calculation of the rate of gas–liquid nucleation has remained largely incomplete despite the existence of reliable results from unbiased simulation studies at large supersaturation. Although the classical nucleation theory formulated by Becker–Doring–Zeldovich about a century ago provides an elegant, widely used picture of nucleation in a first-order phase transition, the theory finds difficulties in predicting the rate accurately, especially in the case of gas-to-liquid nucleation. Here, we use a multiple-order parameter description to construct the nucleation free energy surface needed to calculate the nucleation rate. A multidimensional non-Markovian (MDNM) rate theory formulation that generalizes Langer’s well-known nucleation theory by using the Grote–Hynes MDNM treatment is used to obtain the rate of barrier crossing. We find good agreement of the theory with the rate obtained by direct unbiased molecular dynamics simulations—the latter is feasible at large supersaturation, S. The theory gives an experimentally strong dependence of the rate of nucleation on supersaturation, S. Interestingly, we find a strong influence of the frequency-dependent friction coefficient at the barrier top. This arises from multiple recrossings of the barrier surface. We find that a Markovian theory, such as Langer’s formulation, fails to capture the rate quantitatively. In addition, the multidimensional transition state theory expression performs poorly, revealing the underlying role of the friction coefficient.
尽管在大过饱和度条件下进行的无偏模拟研究已经取得了可靠的结果,但对气液成核速率进行第一性原理理论计算的任务在很大程度上仍未完成。尽管贝克尔-多林-泽尔多维奇(Becker-Doring-Zeldovich)在大约一个世纪前提出的经典成核理论为一阶相变中的成核提供了一个优雅的、被广泛使用的图景,但该理论在准确预测速率方面存在困难,尤其是在气-液成核的情况下。在这里,我们使用多阶参数描述来构建计算成核率所需的成核自由能面。多维非马尔可夫(MDNM)速率理论表述通过使用格罗特-海因斯 MDNM 处理方法对兰格著名的成核理论进行了概括,从而获得了越障速率。我们发现该理论与通过直接无偏分子动力学模拟获得的速率非常吻合--后者在高过饱和度 S 条件下是可行的。这源于阻挡层表面的多次重越。我们发现马尔可夫理论(如朗格公式)无法定量捕捉这一速率。此外,多维过渡态理论表达也表现不佳,揭示了摩擦系数的潜在作用。
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引用次数: 0
Thermodynamics of the gas-phase dimerization of formic acid: Fully anharmonic finite temperature calculations at the CCSD(T) and many DFT levels 甲酸气相二聚化的热力学:在 CCSD(T) 和许多 DFT 水平上进行的全非谐波有限温度计算
Pub Date : 2024-05-01 DOI: 10.1063/5.0205448
Dávid Vrška, Michal Pitoňák, Tomáš Bučko
A proof-of-concept study is undertaken to demonstrate the utility of the machine learning combined with the thermodynamic perturbation theory (MLPT) to test the accuracy of electronic structure methods in finite-temperature thermodynamic calculations. As a test example, formic acid dimer is chosen, which is one of the systems included in the popular benchmark set S22 [Jurečka et al., Phys. Chem. Chem. Phys. 8, 1985–1993 (2006)]. Starting from the explicit molecular dynamics and thermodynamic integration performed at the PBE + D2 level, the MLPT is used to obtain fully anharmonic dimerization free and internal energies at the reference quality CCSD(T) level and 19 different density functional approximations, including GGA, meta-GGA, non-local, and hybrid functionals with and without dispersion corrections. Our finite-temperature results are shown to be both qualitatively and quantitatively different from those obtained using the conventional benchmarking strategy based on fixed structures. The hybrid functional HSE06 is identified as the best performing approximate method tested, with the errors in free and internal energies of dimerization being 36 and 41 meV, respectively.
为了证明机器学习与热力学扰动理论(MLPT)相结合在有限温度热力学计算中测试电子结构方法准确性的实用性,我们进行了一项概念验证研究。我们选择了甲酸二聚物作为测试实例,它是流行的基准集 S22 [Jurečka 等人,《物理化学》(Phys. Chem. Chem. Phys. 8, 1985-1993 (2006)]中的系统之一。从在 PBE + D2 水平上进行的显式分子动力学和热力学积分开始,利用 MLPT 在参考质量 CCSD(T) 水平和 19 种不同的密度泛函近似(包括 GGA、元 GGA、非局部和带或不带色散修正的混合泛函)上获得完全非谐波二聚化自由能和内能。结果表明,我们的有限温度结果与使用基于固定结构的传统基准策略得到的结果在质和量上都有所不同。混合函数 HSE06 被认为是测试中性能最好的近似方法,二聚化的自由能和内能误差分别为 36 和 41 meV。
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引用次数: 0
Switch the click: Ultrafast photochemistry of photoDIBO-OH tracked by time-resolved IR spectroscopy 切换点击通过时间分辨红外光谱追踪光二溴乙烷-OH 的超快光化学过程
Pub Date : 2024-05-01 DOI: 10.1063/5.0196923
L. Denninger, H. Brunst, L. J. G. W. van Wilderen, M. Horz, H. M. A. Masood, C. D. McNitt, I. Burghardt, V. V. Popik, J. Bredenbeck
Click chemistry refers to selective reactions developed for grafting of bio(macro)molecules in their biological media. Caged click compounds have been employed to spatiotemporally control click reactions. Here, we survey the uncaging of photo-dibenzocyclooctyne-OH (photoDIBO-OH) to its click-chemistry active form DIBO-OH, with particular attention to its conversion timescale and efficiency. Ultraviolet pump–infrared probe experiments reveal a stepwise decarbonylation: first, carbon monoxide (C≡O) is released within 1.8 ps, and then, it converts, within 10 ps, to DIBO-OH. Completion of uncaging is achieved with an efficiency of ∼50%. A successful demonstration of two-photon uncaging of photoDIBO-OH at long wavelength (700 nm) confers enhanced in vivo compatibility and proceeds on the same timescale.
点击化学是指为在生物介质中接枝生物(大)分子而开发的选择性反应。笼式点击化合物已被用于时空控制点击反应。在此,我们研究了将光二苯并环辛炔-OH(photoDIBO-OH)解笼为其点击化学活性形式 DIBO-OH的过程,并特别关注其转化时间尺度和效率。紫外泵-红外探针实验揭示了一种逐步脱羰基的过程:首先,一氧化碳(C≡O)在 1.8 ps 内释放,然后,在 10 ps 内转化为 DIBO-OH。完成解笼的效率高达 50%。在长波长(700 nm)下成功演示了双光子释放光DIBO-OH,增强了其在体内的兼容性,并以相同的时间尺度进行。
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引用次数: 0
Energy decomposition analysis method using density matrix formulation 使用密度矩阵公式的能量分解分析方法
Pub Date : 2024-05-01 DOI: 10.1063/5.0202787
Yueyang Zhang, Longxiang Yan, Wei Wu, Peifeng Su
In this work, an energy decomposition analysis (EDA) method with the strategy of density matrix, called DM-EDA, is proposed on the basis of single reference electronic structure calculations. Different from traditional EDA methods, instead of an intermediate state wave function, the EDA terms in DM-EDA are expressed in the forms of the density matrix. This method can be carried out with various kinds of density matrices. With the efficient implementation, DM-EDA not only greatly improves the computational efficiency but also provides quantitative knowledge of intermolecular interactions with a large number of monomers.
本文在单参比电子结构计算的基础上,提出了一种采用密度矩阵策略的能量分解分析(EDA)方法,称为 DM-EDA。与传统的 EDA 方法不同,DM-EDA 中的 EDA 项不是中间态波函数,而是用密度矩阵的形式表示。这种方法可以用各种密度矩阵来实现。通过高效实施,DM-EDA 不仅大大提高了计算效率,还能定量了解大量单体的分子间相互作用。
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引用次数: 0
Prediction through quantum dynamics simulations: Photo-excited cyclobutanone 通过量子动力学模拟进行预测:光激发环丁酮
Pub Date : 2024-05-01 DOI: 10.1063/5.0203654
Olivia Bennett, Antonia Freibert, K. Eryn Spinlove, Graham A. Worth
Quantum dynamics simulations are becoming a standard tool for simulating photo-excited molecular systems involving a manifold of coupled states, known as non-adiabatic dynamics. While these simulations have had many successes in explaining experiments and giving details of non-adiabatic transitions, the question remains as to their predictive power. In this work, we present a set of quantum dynamics simulations on cyclobutanone using both grid-based multi-configuration time-dependent Hartree and direct dynamics variational multi-configuration Gaussian methods. The former used a parameterized vibronic coupling model Hamiltonian, and the latter generated the potential energy surfaces on the fly. The results give a picture of the non-adiabatic behavior of this molecule and were used to calculate the signal from a gas-phase ultrafast electron diffraction (GUED) experiment. Corresponding experimental results will be obtained and presented at a later stage for comparison to test the predictive power of the methods. The results show that over the first 500 fs after photo-excitation to the S2 state, cyclobutanone relaxes quickly to the S1 state, but only a small population relaxes further to the S0 state. No significant transfer of population to the triplet manifold is found. It is predicted that the GUED experiments over this time scale will see signals related mostly to the C–O stretch motion and elongation of the molecular ring along the C–C–O axis.
量子动力学模拟正逐渐成为模拟光激发分子系统的标准工具,该系统涉及多方面的耦合状态,即所谓的非绝热动力学。虽然这些模拟在解释实验和提供非绝热转变细节方面取得了许多成功,但其预测能力仍然是个问题。在这项工作中,我们采用基于网格的多构型时变哈特里方法和直接动力学变分多构型高斯方法,对环丁酮进行了一组量子动力学模拟。前者使用参数化的振子耦合模型哈密顿,后者则直接生成势能面。研究结果展示了该分子的非绝热行为,并用于计算气相超快电子衍射(GUED)实验的信号。相应的实验结果将在稍后阶段获得和展示,以便进行比较,检验这些方法的预测能力。结果表明,在光激发到 S2 状态后的最初 500 fs 内,环丁酮迅速弛豫到 S1 状态,但只有一小部分种群进一步弛豫到 S0 状态。在三重流形中没有发现明显的种群转移。据预测,在这一时间范围内进行的 GUED 实验将发现主要与 C-O 伸展运动和分子环沿 C-C-O 轴伸长有关的信号。
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引用次数: 0
Simple and efficient methods for local structural analysis in polydisperse hard disk systems 用于多分散硬盘系统局部结构分析的简单高效方法
Pub Date : 2024-05-01 DOI: 10.1063/5.0194873
Daigo Mugita, Kazuyoshi Souno, Hiroaki Koyama, Taisei Nakamura, Masaharu Isobe
In nonequilibrium statistical physics, quantifying the nearest (and higher-order) neighbors and free volumes of particles in many-body systems is crucial to elucidating the origin of macroscopic collective phenomena, such as glass/granular jamming transitions and various aspects of the behavior of active matter. However, conventional techniques (based on a fixed-distance cutoff or the Voronoi construction) have mainly been applied to equilibrated, homogeneous, and monodisperse particle systems. In this paper, we implement simple and efficient methods for local structure analysis in nonequilibrium, inhomogeneous, and polydisperse hard disk systems. We show how these novel methods can overcome the difficulties encountered by conventional techniques as well as demonstrate some applications.
在非平衡统计物理学中,量化多体系统中粒子的近邻(和高阶)和自由体积对于阐明宏观集体现象的起源至关重要,例如玻璃/粒状干扰转换和活性物质行为的各个方面。然而,传统技术(基于固定距离截止或 Voronoi 结构)主要应用于平衡、均质和单分散粒子系统。在本文中,我们采用简单高效的方法,对非平衡、不均匀和多分散硬盘系统进行局部结构分析。我们展示了这些新方法如何克服传统技术遇到的困难,并演示了一些应用。
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引用次数: 0
Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP 通过 LICHEM、Psi4 和 Tinker-HP 将基于密度的力场 GEM 无缝集成到 QM/MM 模拟中
Pub Date : 2024-05-01 DOI: 10.1063/5.0200722
Jorge Nochebuena, Andrew C. Simmonett, G. Andrés Cisneros
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method’s proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant.
量子力学/分子力学(QM/MM)混合模拟已成为计算化学,尤其是分析复杂生物和凝聚相系统的重要工具。在此基础上,我们的工作在 QM/MM 框架内提出了高斯静电模型(GEM)的新实施方案,这是一种基于密度的可极化力场。这一进步实现了无缝集成,使用 LICHEM 代码只需一步就能进行高效和优化的 QM/GEM 计算。我们已经成功地将我们的实现应用于水二聚体和六聚体,证明了我们有能力处理具有不同数量水分子的水系统。此外,我们还扩展了应用范围,描述了天冬氨酸二聚体在一盒水中的双质子转移,这凸显了该方法在研究异质系统方面的能力。我们的方法可以灵活地进行即时密度拟合或利用预拟合系数来估计交换和库仑贡献。这种灵活性提高了分子相互作用建模的效率和准确性,尤其是在极化效应显著的体系中。
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引用次数: 0
Insights into thiocyanate-enhanced photoluminescence in CsPbBr3 nanocrystals by ultrafast two-dimensional infrared spectroscopy 通过超快二维红外光谱深入了解硫氰酸盐增强的 CsPbBr3 纳米晶体中的光致发光
Pub Date : 2024-05-01 DOI: 10.1063/5.0200873
Arghyadeep Basu, Nathan Rafisiman, Saar Shaek, Rachel Lifer, Vivek Yadav, Yaron Kauffmann, Yehonadav Bekenstein, Lev Chuntonov
Functionalization of perovskite nanocrystal surfaces with thiocyanate anions presents a transformative approach to enhancing stability and photoluminescence quantum yield (PLQY) through surface defect passivation. This study investigates the role of thiocyanate ligands in modifying the optoelectronic properties of CsPbBr3 nanocrystals. We employed ultrafast two-dimensional infrared spectroscopy to investigate the nature of the dynamic interaction of thiocyanate ligands with nanocrystal surfaces, providing insights into the mechanisms underlying the observed increase in PLQY and stability. Our analysis reveals that the thiocyanate ligands efficiently passivate the surface defects, thereby enhancing the PLQY and the stability of the treated nanocrystals. The spectroscopic evidence supports a model where thiocyanate binds to under-coordinated lead atoms, contributing to a stable nanocrystal surface with enhanced optoelectronic performance. This ligand-induced passivation mechanism advances our understanding of surface chemistry's role in optimizing nanomaterials for solar cell and LED applications.
用硫氰酸根阴离子对包晶石纳米晶体表面进行功能化处理,是通过表面缺陷钝化提高稳定性和光致发光量子产率(PLQY)的一种变革性方法。本研究探讨了硫氰酸配体在改变 CsPbBr3 纳米晶体光电特性中的作用。我们采用超快二维红外光谱来研究硫氰酸配体与纳米晶体表面动态相互作用的性质,从而深入了解观察到的 PLQY 和稳定性增加的内在机制。我们的分析表明,硫氰酸配体有效地钝化了表面缺陷,从而提高了经处理的纳米晶体的 PLQY 和稳定性。光谱证据支持这样一种模型:硫氰酸盐与配位不足的铅原子结合,有助于形成稳定的纳米晶体表面,从而提高光电性能。这种配体诱导的钝化机制加深了我们对表面化学在优化太阳能电池和 LED 应用纳米材料中的作用的理解。
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引用次数: 0
Exploring electron donor and acceptor effects: DFT analysis of ESIPT/GSIPT in 2-(oxazolinyl)-phenols for photophysical and luminophore enhancement 探索电子供体和受体效应:DFT 分析 2-(噁唑啉基)-苯酚中的 ESIPT/GSIPT 对光物理和发光体的增强作用
Pub Date : 2024-05-01 DOI: 10.1063/5.0202890
Murugesan Panneerselvam, Reshma Rensil Francis, Singaravel Nathiya, Rajadurai Vijay Solomon, Madhavan Jaccob, Luciano T. Costa
Understanding excited-state intramolecular proton transfer (ESIPT) is essential for designing organic molecules to enhance photophysical and luminophore properties in the development of optoelectronic devices. In this context, an attempt has been made to understand the impact of substituents on the ESIPT process of 2-(oxazolinyl)-phenol. Electron donating (EDG: –NH2, –OCH3, and –CH3) and electron withdrawing (EWG: –Cl, –Br, –COOH, –CF3, –CN, and –NO2) substitutions have been computationally designed and screened through density functional theory (DFT) and time-dependent density-functional theory (TDDFT) calculations. Furthermore, the ground state intramolecular proton transfer and ESIPT mechanisms of these designed luminophores are explored using the transition state theory. The results reveal that molecules with EDG show higher absorption and emission peaks than molecules with EWG and also indicate that the mobility of charge carriers in 2-(oxazolinyl)-phenol derivatives is significantly influenced by substituents. We found that the EWGs decrease the reorganization energy and increase the vertical ionization potential and electron affinity values, as well as the highest occupied molecular orbital-lowest unoccupied molecular orbital gap, compared to the EDG substituted molecules. Significantly, the excited state (S1) of the keto emission (K) form shows notably larger values for the EDG substitutions. The intersystem crossing pathway efficiency weakens with reduced spin–orbit coupling matrix element in the enol form with electron-donating substituents and vice versa in the keto form during S1–T3 transitions. Our research links intramolecular proton transfers and triplet generation, making these substituted molecules appealing for optoelectronic devices. Introducing EDGs, such as –NH2, boosts the ESIPT reaction in 2-(oxazolinyl)-phenol. This study guides designing ESIPT emitters with unique photophysical properties.
了解激发态分子内质子转移(ESIPT)对于设计有机分子以增强光电器件开发过程中的光物理和发光特性至关重要。为此,我们尝试了解取代基对 2-(噁唑啉基)-苯酚 ESIPT 过程的影响。通过密度泛函理论(DFT)和时变密度泛函理论(TDDFT)计算,设计并筛选了电子捐赠(EDG:-NH2、-OCH3 和 -CH3)和电子撤回(EWG:-Cl、-Br、-COOH、-CF3、-CN 和 -NO2)取代基。此外,还利用过渡态理论探讨了这些设计的发光体的基态分子内质子转移和 ESIPT 机制。研究结果表明,具有 EDG 的分子比具有 EWG 的分子显示出更高的吸收峰和发射峰,同时还表明 2-(恶唑啉基)-苯酚衍生物中电荷载流子的迁移率受到取代基的显著影响。我们发现,与 EDG 取代的分子相比,EWG 降低了重组能,增加了垂直电离势和电子亲和值,以及最高占有分子轨道-最低未占有分子轨道间隙。值得注意的是,在 EDG 取代的分子中,酮发射(K)形式的激发态(S1)值明显更大。在 S1-T3 转换过程中,随着带有电子捐赠取代基的烯醇形式的自旋轨道耦合矩阵元素的减少,系统间交叉途径的效率也会减弱,反之亦然。我们的研究将分子内质子转移和三重子生成联系起来,使这些取代分子成为光电器件的理想选择。引入 EDG(如 -NH2)可促进 2-(恶唑啉基)-苯酚中的 ESIPT 反应。这项研究为设计具有独特光物理性质的 ESIPT 发射器提供了指导。
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引用次数: 0
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The Journal of Chemical Physics
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