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Tribute to Xueming Yang 向杨学明致敬
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 DOI: 10.1021/acs.jpca.4c0705910.1021/acs.jpca.4c07059
Dong H. Zhang*, Xingan Wang, Mingfei Zhou and Feng Gai, 
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引用次数: 0
Enhanced Catalytic Probe Design for Mapping Radical Density in the Plasma Afterglow. 用于绘制等离子体余辉中自由基密度的增强型催化探针设计。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-11 DOI: 10.1021/acs.jpca.4c06195
Anja Herrmann, Patrick M Krebaum, Susanta Bera, Mihalis N Tsampas, Mauritius C M van de Sanden

The electrification of chemical processes using plasma generates an increasing demand for sensors, monitoring concentrations of plasma-activated species such as radicals. Radical probes are a low-cost in situ method for spatially resolved quantification of the radical density in a plasma afterglow using the heat from the exothermal recombination of radicals on a catalytic surface. However, distinguishing recombination heating from other heat fluxes in the system is challenging. In this study, we present a heat flux analysis based on probe measurements inside the reactor, with simultaneous IR imaging monitoring of the temperature of the reactor wall. The impact of radiation heat on a single thermocouple as well as the advantage of a dual thermocouple setup (using a catalytic unit together with a reference thermocouple) is shown. We add a heat sink with a monitored temperature to the dual thermocouple setup, allowing the determination of conductive and radiative heat fluxes. The heat sink gives more information on the measurement and reduces ambiguities in the evaluation used by others. The probe was tested by mapping N atom densities throughout the plasma afterglow of our reactor, enabling evaluation of the recombination kinetics of the radicals in the gas phase. Three-body recombination was shown to be the main pathway of recombination, with a recombination rate of krec = (2.0 ± 0.9)·10-44 m6/s, which is in line with the known literature findings, demonstrating that the measured species are N radicals and the probe did not influence the plasma or recombination reactions in the afterglow.

利用等离子体实现化学过程的电气化,对传感器的需求与日俱增,以监测等离子体活化物种(如自由基)的浓度。自由基探针是一种低成本的原位方法,利用催化表面自由基放热重组产生的热量,对等离子体余辉中的自由基密度进行空间分辨量化。然而,将重组加热与系统中的其他热通量区分开来具有挑战性。在本研究中,我们提出了一种基于反应器内探针测量的热通量分析方法,并同时对反应器壁的温度进行了红外成像监测。研究显示了辐射热对单个热电偶的影响以及双热电偶设置(使用催化装置和参考热电偶)的优势。我们在双热电偶装置中添加了一个可监测温度的散热器,从而可以确定传导热通量和辐射热通量。散热器提供了更多的测量信息,减少了他人评估中的模糊性。通过绘制反应器等离子体余辉中的 N 原子密度图,对探针进行了测试,从而评估了气相中自由基的重组动力学。结果表明,三体重组是重组的主要途径,重组率为 krec = (2.0 ± 0.9)-10-44 m6/s,这与已知的文献研究结果一致,表明测量到的物种是 N 自由基,探针不会影响余辉中的等离子体或重组反应。
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引用次数: 0
Toward the Rational Design of an OsM4 Center for Methane Activation: Gas-Phase Result-Derived Neural Network Model. 合理设计用于甲烷活化的 OsM4 中心:气相结果神经网络模型。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-14 DOI: 10.1021/acs.jpca.4c06289
Shihan Li, Jiaying Wang, Chao Qian, Shaodong Zhou

Gas-phase reactions of [OsBx]+ (x = 1-4) with methane at ambient temperature have been studied by using quadrupole-ion trap mass spectrometry combined with quantum chemical calculations. The [OsBx]+ (x = 1-4) cluster ions can undergo dehydrogenation reactions with methane. Comprehensive analysis of the [OsBx]+/CH4 (x = 1-4) system with Os-complexes ([OsCy]+ (y = 1-3) and [OsOz]+ (z = 1-3)) shows that the large polarity of the cluster and the high sum of the pair energies between Os and the ligand in the ETS-NOCV combine to promote the ability of the cluster to activate methane. Cluster polarity may induce heterolytic cleavage of the C-H bond, and the sum of the pair energies of the fragments may reduce the cluster orbital energy to match the methane orbital and improve the cluster stability. The synergistic interplay of these two factors may offer a viable approach for the activation of methane in the condensed phase, which involves modulating the coordination environment of the active sites to enhance the stability and facilitate C-H bond cleavage and the degree of matching with methane orbitals. A nonlinear function is used to extract second-order characteristic features that have a significant impact on the energy difference based on the limited energy difference data of the OsBmCnOlHk units. A neural network model is next designed to predict the reaction barrier for methane conversion by OsM4+ (M = C, N, O, Al, Si, or P) with high accuracy.

利用四极杆离子阱质谱结合量子化学计算,研究了[OsBx]+(x = 1-4)与甲烷在环境温度下的气相反应。OsBx]+(x = 1-4)团簇离子可与甲烷发生脱氢反应。对[OsBx]+/CH4 (x = 1-4)体系与 Os-络合物([OsCy]+ (y = 1-3) 和 [OsOz]+ (z = 1-3))的综合分析表明,簇离子的极性大和 ETS-NOCV 中 Os 与配体之间的配对能量总和高,共同促进了簇离子活化甲烷的能力。簇的极性可诱导 C-H 键的异质裂解,碎片的对能之和可降低簇的轨道能,使之与甲烷轨道相匹配,从而提高簇的稳定性。这两个因素的协同作用可能为在凝聚相中活化甲烷提供了一种可行的方法,即通过调节活性位点的配位环境来提高稳定性,促进 C-H 键的裂解以及与甲烷轨道的匹配程度。根据 OsBmCnOlHk 单元的有限能差数据,使用非线性函数提取对能差有显著影响的二阶特征。接下来设计了一个神经网络模型,以高精度预测 OsM4+(M = C、N、O、Al、Si 或 P)转化甲烷的反应障碍。
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引用次数: 0
Tribute to Xueming Yang. 向杨学明致敬
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 DOI: 10.1021/acs.jpca.4c07059
Dong H Zhang, Xingan Wang, Mingfei Zhou, Feng Gai
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引用次数: 0
Balancing Brightness and Photobasicity: Modulating Excited-State Proton Transfer Pathways in Push-Pull Fluorophores for Biological Two-Photon Imaging. 平衡亮度与光碱度:调节推拉荧光团中的激发态质子转移途径,实现生物双光子成像。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-07 DOI: 10.1021/acs.jpca.4c05649
Adam M McCallum, Jiyao Yu, S Sumalekshmy, Abigail Hagwood, Christoph J Fahrni

Push-pull fluorophores with donor-π-acceptor architectures are attractive scaffolds for the design of probes and labels for two-photon microscopy. Such fluorophores undergo a significant charge-delocalization in the excited state, which is essential for achieving a large two-photon absorption cross-section and brightness. The polarized excited state may, however, also facilitate excited-state proton transfer (ESPT) pathways that can interfere with the probe response. Herein, we employed steady-state and time-resolved spectroscopic studies to elucidate whether ESPT is responsible for the pH-dependent emission response of the Zn(II)-selective fluorescent probe chromis-1. Composed of a push-pull architecture with a pyridine ring as the acceptor, the chromis-1 fluorophore core acts as a photobase that promotes ESPT upon acidification. Although the pKa of the pyridine acceptor increases more than six orders of magnitude upon excitation, the photobasicity is not sufficient to deprotonate solvent water molecules under neutral conditions. Rather, the pH-dependent emission response is caused by the pendant bis-isonicotinic acid chelating group which upon protonation facilitates an excited-state intramolecular proton transfer to the pyridine acceptor. A simple permutation of the core pyridine nitrogen from the para- to the ortho-position relative to the thiazole substituent was sufficient to reduce the excited-state basicity by two orders of magnitude without compromising the two-photon excited brightness. These results highlight the importance of choosing the appropriate fluorophore core and chelating moiety for minimizing pH-dependent responses in the design of fluorescent probes for biological imaging.

具有供体-π-受体结构的推拉荧光团是设计双光子显微镜探针和标签的极具吸引力的支架。这类荧光团在激发态会发生显著的电荷异化,这对于获得较大的双光子吸收截面和亮度至关重要。然而,极化激发态也可能促进激发态质子转移(ESPT)途径,从而干扰探针的响应。在此,我们采用稳态和时间分辨光谱研究来阐明 ESPT 是否是 Zn(II)选择性荧光探针 chromis-1 的 pH 依赖性发射响应的原因。chromis-1 的荧光团核心由一个吡啶环作为受体的推拉结构组成,在酸化时可作为光碱促进 ESPT。虽然吡啶受体的 pKa 在激发时会增加六个数量级,但在中性条件下,光碱度不足以使溶剂水分子去质子化。相反,与 pH 值相关的发射反应是由悬垂的双异烟酸螯合基团引起的,该基团在质子化时会促进激发态分子内质子向吡啶受体的转移。相对于噻唑取代基,只需将核心吡啶氮从对位变为正位,就足以将激发态碱性降低两个数量级,而不会影响双光子激发亮度。这些结果凸显了在设计用于生物成像的荧光探针时,选择适当的荧光团核心和螯合基团以尽量减少 pH 依赖性反应的重要性。
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引用次数: 0
Autobiography of Xueming Yang. 杨学明自传》。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 DOI: 10.1021/acs.jpca.4c07061
Xueming Yang
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引用次数: 0
Measurements of the Rovibrationally Dependent Lifetimes of C2 in the 13Σg+ and f3Σg- States through the VUV-Pump-UV-Probe Scheme. 通过紫外-泵-紫外-探针方案测量 13Σg+ 和 f3Σg- 态中 C2 的振动相关寿命。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 DOI: 10.1021/acs.jpca.4c06785
Liying Ma, Di Li, Pan Jiang, Min Cheng, Hong Gao

The dicarbon molecule, C2, is one of the most important diatomic species in various gaseous environments. Despite extensive spectroscopic studies in the last two centuries, the radiative and photodissociative properties of C2 in its highly excited electronic states are still largely unexplored, particularly in the short vacuum ultraviolet (VUV) region. In this study, the lifetimes of C2 for rotational levels in the recently identified 13Σg+ state up to the vibrational level ν' = 4 and in the f3Σg- state up to ν' = 2 are measured for the first time with a VUV-pump-UV-probe photoionization scheme. It is found that all rovibrational levels in the f3Σg- state have lifetimes shorter than the dynamical limit of ∼4.7 ns of the present method, and the lifetimes in the 13Σg+ state show obvious and complex dependence on the rotational and vibrational quantum levels. Generally, the lifetime in the 13Σg+ state becomes shorter at higher rotational and vibrational levels, i.e., the longest lifetime measured in the ν' = 0 level is ∼18 ns, while all rotational levels in the ν' = 4 level are found to have shorter lifetimes than ∼4.7 ns. This implies that predissociation might occur and become more prominent at the higher energy levels in the 13Σg+ state. The prominent dependence of the lifetime on the rotational, vibrational and electronic level indicates complex dynamical processes in the highly excited states of C2.

二碳分子 C2 是各种气态环境中最重要的二原子物种之一。尽管在过去的两个世纪中进行了大量的光谱研究,但 C2 在其高度激发的电子态中的辐射和光解离特性在很大程度上仍未得到探索,尤其是在短真空紫外(VUV)区域。在本研究中,首次采用 VUV-泵-紫外探针光离子化方案测量了 C2 在最近确定的 13Σg+ 态至振动水平 ν' = 4 和 f3Σg- 态至 ν' = 2 的旋转水平的寿命。研究发现,f3Σg-态的所有旋转振动水平的寿命都短于本方法的动力学极限 ∼ 4.7 ns,而 13Σg+ 态的寿命与旋转和振动量子水平有明显而复杂的依赖关系。一般来说,旋转和振动水平越高,13Σg+态的寿命越短,即在ν' = 0水平测得的最长寿命为∼18 ns,而在ν' = 4水平的所有旋转水平的寿命都短于∼4.7 ns。这意味着在 13Σg+ 态的高能级上可能会发生预解离,而且会变得更加突出。寿命对旋转、振动和电子水平的显著依赖性表明 C2 的高激发态具有复杂的动力学过程。
{"title":"Measurements of the Rovibrationally Dependent Lifetimes of C<sub>2</sub> in the 1<sup>3</sup>Σ<sub>g</sub><sup>+</sup> and <i>f</i><sup>3</sup>Σ<sub>g</sub><sup>-</sup> States through the VUV-Pump-UV-Probe Scheme.","authors":"Liying Ma, Di Li, Pan Jiang, Min Cheng, Hong Gao","doi":"10.1021/acs.jpca.4c06785","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c06785","url":null,"abstract":"<p><p>The dicarbon molecule, C<sub>2</sub>, is one of the most important diatomic species in various gaseous environments. Despite extensive spectroscopic studies in the last two centuries, the radiative and photodissociative properties of C<sub>2</sub> in its highly excited electronic states are still largely unexplored, particularly in the short vacuum ultraviolet (VUV) region. In this study, the lifetimes of C<sub>2</sub> for rotational levels in the recently identified 1<sup>3</sup>Σ<sub>g</sub><sup>+</sup> state up to the vibrational level ν' = 4 and in the <i>f</i><sup>3</sup>Σ<sub>g</sub><sup>-</sup> state up to ν' = 2 are measured for the first time with a VUV-pump-UV-probe photoionization scheme. It is found that all rovibrational levels in the <i>f</i><sup>3</sup>Σ<sub>g</sub><sup>-</sup> state have lifetimes shorter than the dynamical limit of ∼4.7 ns of the present method, and the lifetimes in the 1<sup>3</sup>Σ<sub>g</sub><sup>+</sup> state show obvious and complex dependence on the rotational and vibrational quantum levels. Generally, the lifetime in the 1<sup>3</sup>Σ<sub>g</sub><sup>+</sup> state becomes shorter at higher rotational and vibrational levels, i.e., the longest lifetime measured in the ν' = 0 level is ∼18 ns, while all rotational levels in the ν' = 4 level are found to have shorter lifetimes than ∼4.7 ns. This implies that predissociation might occur and become more prominent at the higher energy levels in the 1<sup>3</sup>Σ<sub>g</sub><sup>+</sup> state. The prominent dependence of the lifetime on the rotational, vibrational and electronic level indicates complex dynamical processes in the highly excited states of C<sub>2</sub>.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantum Chemistry Study on Cl-Initiated Reactions of 2-Chloropropane and 2-Methylpropanoyl Halogen (Cl, Br, F): Mechanism, Kinetics, and Atmospheric Implications. Cl 引发的 2-氯丙烷和 2-甲基丙酰基卤素(Cl、Br、F)反应的量子化学研究:机理、动力学和对大气的影响。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-13 DOI: 10.1021/acs.jpca.4c06130
Wan-Ying Yu, Tai-Xing Chi, Shuang Ni, Xiang-Huan Liu, Ting-Ting Meng, Xiao-Ming Song, Ke Zhang, Yi-Chen Wang, Feng-Yang Bai, Zhen Zhao

Halogenated volatile organic compounds (HVOCs) pose significant bioaccumulative and toxicological risks, necessitating effective strategies for their removal. Here, we show, through a computational study employing density functional theory and coupled cluster methods, the detailed mechanism and kinetic properties of Cl-initiated degradation reactions of 2-chloropropane (2-CP, (CH3)2CHCl) and 2-methylpropanoyl halide ((CH3)2CHCOX, X = Cl, Br, F). The reaction rate constants of all the channels were calculated by the canonical variational transition state theory (CVT) with the correction of the small curvature tunneling effect (SCT) at 200-1000 K. The subsequent transformation pathways of the major radical products of (CH3)2CHCl and (CH3)2CHCOCl in the presence of O2, NO, and HO2 radical were investigated. The results elucidate the reaction pathways and rate constants, which are in excellent agreement with the experimental data at 296 K. We further explore the atmospheric implications of these reactions by assessing the atmospheric lifetime (τ) and ozone depletion potential (ODP). Additionally, we delve into the aquatic toxicity and bioaccumulation potential of the reactants and their transformation products. This study not only advances our knowledge of the atmospheric fate of halogenated hydrocarbons but also underscores the importance of considering the environmental and toxicological impacts in the development of HVOC mitigation strategies.

卤代挥发性有机化合物(HVOCs)具有重大的生物累积性和毒理学风险,因此必须采取有效的策略来清除它们。在此,我们通过采用密度泛函理论和耦合簇方法进行计算研究,展示了由氯引发的 2-氯丙烷(2-CP,(CH3)2CHCl)和 2-甲基丙酰基卤化物((CH3)2CHCOX,X = Cl、Br、F)降解反应的详细机理和动力学特性。研究了在 O2、NO 和 HO2 自由基存在下,(CH3)2CHCl 和 (CH3)2CHCOCl 的主要自由基产物的后续转化途径。通过评估大气寿命(τ)和臭氧消耗潜能(ODP),我们进一步探讨了这些反应对大气的影响。此外,我们还深入研究了反应物及其转化产物的水生毒性和生物累积潜力。这项研究不仅增进了我们对卤代烃大气归宿的了解,还强调了在制定 HVOC 减排战略时考虑环境和毒理学影响的重要性。
{"title":"Quantum Chemistry Study on Cl-Initiated Reactions of 2-Chloropropane and 2-Methylpropanoyl Halogen (Cl, Br, F): Mechanism, Kinetics, and Atmospheric Implications.","authors":"Wan-Ying Yu, Tai-Xing Chi, Shuang Ni, Xiang-Huan Liu, Ting-Ting Meng, Xiao-Ming Song, Ke Zhang, Yi-Chen Wang, Feng-Yang Bai, Zhen Zhao","doi":"10.1021/acs.jpca.4c06130","DOIUrl":"10.1021/acs.jpca.4c06130","url":null,"abstract":"<p><p>Halogenated volatile organic compounds (HVOCs) pose significant bioaccumulative and toxicological risks, necessitating effective strategies for their removal. Here, we show, through a computational study employing density functional theory and coupled cluster methods, the detailed mechanism and kinetic properties of Cl-initiated degradation reactions of 2-chloropropane (2-CP, (CH<sub>3</sub>)<sub>2</sub>CHCl) and 2-methylpropanoyl halide ((CH<sub>3</sub>)<sub>2</sub>CHCOX, X = Cl, Br, F). The reaction rate constants of all the channels were calculated by the canonical variational transition state theory (CVT) with the correction of the small curvature tunneling effect (SCT) at 200-1000 K. The subsequent transformation pathways of the major radical products of (CH<sub>3</sub>)<sub>2</sub>CHCl and (CH<sub>3</sub>)<sub>2</sub>CHCOCl in the presence of O<sub>2</sub>, NO, and HO<sub>2</sub> radical were investigated. The results elucidate the reaction pathways and rate constants, which are in excellent agreement with the experimental data at 296 K. We further explore the atmospheric implications of these reactions by assessing the atmospheric lifetime (τ) and ozone depletion potential (ODP). Additionally, we delve into the aquatic toxicity and bioaccumulation potential of the reactants and their transformation products. This study not only advances our knowledge of the atmospheric fate of halogenated hydrocarbons but also underscores the importance of considering the environmental and toxicological impacts in the development of HVOC mitigation strategies.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"9972-9985"},"PeriodicalIF":2.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Semiclassical Transition State Theory (SCTST) Rate Coefficients for the Unimolecular Decomposition of the Ethoxy (CH3CH2O) Radical. 乙氧基 (CH3CH2O) 自由基单分子分解的半经典过渡态理论 (SCTST) 速率系数。
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-12 DOI: 10.1021/acs.jpca.4c05775
Thanh Lam Nguyen, Gregory H Jones, Bryan Changala, Binod Raj Giri, John R Barker, John F Stanton

The thermal unimolecular decay of ethoxy is important in high-temperature combustion environments where the ethoxy radical is a key reactive intermediate. Two dissociation pathways of ethoxy, including the β-C-C scission to yield CH3 + CH2O and the H-elimination to make H + CH3CHO, were characterized using a high-level coupled-cluster-based composite quantum chemical method (mHEAT-345(QΛ)). The former route is found to be dominant while the latter is insignificant, in agreement with previous experimental and theoretical studies. Thermal rate coefficients are calculated for P = 0.001-658 atm (of air) and T = 300-2500 K using semiclassical transition state theory (SCTST) in combination with a pragmatic two-dimensional E,J-resolved master equation (2DME). The effects of tunneling and anharmonicity on the calculated rate constants are also examined. The tunneling factor is found to be inversely dependent on pressure, contrary to previous observations of pressure-dependent tunneling in entrance channels.

乙氧基的单分子热衰变在高温燃烧环境中非常重要,因为乙氧基自由基是一种关键的反应中间体。利用基于高水平耦合簇的复合量子化学方法(mHEAT-345(QΛ))表征了乙氧基的两种解离途径,包括β-C-C 裂解生成 CH3 + CH2O 和 H-消除生成 H + CH3CHO。结果发现前一种途径占主导地位,而后一种途径并不重要,这与之前的实验和理论研究结果一致。在 P = 0.001-658 atm(空气)和 T = 300-2500 K 的条件下,使用半经典过渡态理论(SCTST)结合实用的二维 E、J 分辨主方程(2DME)计算了热速率系数。此外,还考察了隧穿和非谐波对计算速率常数的影响。研究发现隧道因子与压力成反比,这与之前在入口通道中观察到的压力依赖性隧道效应相反。
{"title":"Semiclassical Transition State Theory (SCTST) Rate Coefficients for the Unimolecular Decomposition of the Ethoxy (CH<sub>3</sub>CH<sub>2</sub>O) Radical.","authors":"Thanh Lam Nguyen, Gregory H Jones, Bryan Changala, Binod Raj Giri, John R Barker, John F Stanton","doi":"10.1021/acs.jpca.4c05775","DOIUrl":"10.1021/acs.jpca.4c05775","url":null,"abstract":"<p><p>The thermal unimolecular decay of ethoxy is important in high-temperature combustion environments where the ethoxy radical is a key reactive intermediate. Two dissociation pathways of ethoxy, including the β-C-C scission to yield CH<sub>3</sub> + CH<sub>2</sub>O and the H-elimination to make H + CH<sub>3</sub>CHO, were characterized using a high-level coupled-cluster-based composite quantum chemical method (mHEAT-345(Q<sub>Λ</sub>)). The former route is found to be dominant while the latter is insignificant, in agreement with previous experimental and theoretical studies. Thermal rate coefficients are calculated for <i>P</i> = 0.001-658 atm (of air) and <i>T</i> = 300-2500 K using semiclassical transition state theory (SCTST) in combination with a pragmatic two-dimensional <i>E</i>,<i>J</i>-resolved master equation (2DME). The effects of tunneling and anharmonicity on the calculated rate constants are also examined. The tunneling factor is found to be inversely dependent on pressure, contrary to previous observations of pressure-dependent tunneling in entrance channels.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"9998-10008"},"PeriodicalIF":2.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modulating Coarse-Grained Dynamics by Perturbing Free Energy Landscapes. 通过扰动自由能景观调节粗粒度动力学
IF 2.7 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-21 Epub Date: 2024-11-14 DOI: 10.1021/acs.jpca.4c04530
Ishan Nadkarni, Jinu Jeong, Bugra Yalcin, Narayana R Aluru

We introduce an approach to describe the long-time dynamics of multiatomic molecules by modulating the free energy landscape (FEL) to capture dominant features of the energy-barrier crossing dynamics of the all-atom (AA) system. Notably, we establish that the self-diffusion coefficient of coarse-grained (CG) systems can be accurately delineated by enhancing conservative force fields with high-frequency perturbations. Using theoretical arguments, we show that these perturbations do not alter the lower-order distribution functions, thereby preserving the structure of the AA system after coarse-graining. We demonstrate the utility of this approach using molecular dynamics simulations of simple molecules in bulk with distinct dynamical characteristics with and without time scale separations as well as for inhomogeneous systems where a fluid is confined in a slit-like nanochannel. Additionally, we also apply our approach to more powerful many-body potentials optimized by using machine learning (ML).

我们介绍了一种通过调节自由能景观(FEL)来描述多原子分子长时动力学的方法,以捕捉全原子(AA)系统能障穿越动力学的主要特征。值得注意的是,我们发现粗粒度(CG)系统的自扩散系数可以通过增强保守力场的高频扰动来精确划定。通过理论论证,我们证明这些扰动不会改变低阶分布函数,从而保留了粗粒化后 AA 系统的结构。我们用分子动力学模拟了具有和不具有时间尺度分离的不同动力学特征的简单大分子,以及流体被限制在狭缝状纳米通道中的非均质系统,证明了这种方法的实用性。此外,我们还将我们的方法应用于通过机器学习(ML)优化的更强大的多体势能。
{"title":"Modulating Coarse-Grained Dynamics by Perturbing Free Energy Landscapes.","authors":"Ishan Nadkarni, Jinu Jeong, Bugra Yalcin, Narayana R Aluru","doi":"10.1021/acs.jpca.4c04530","DOIUrl":"10.1021/acs.jpca.4c04530","url":null,"abstract":"<p><p>We introduce an approach to describe the long-time dynamics of multiatomic molecules by modulating the free energy landscape (FEL) to capture dominant features of the energy-barrier crossing dynamics of the all-atom (AA) system. Notably, we establish that the self-diffusion coefficient of coarse-grained (CG) systems can be accurately delineated by enhancing conservative force fields with high-frequency perturbations. Using theoretical arguments, we show that these perturbations do not alter the lower-order distribution functions, thereby preserving the structure of the AA system after coarse-graining. We demonstrate the utility of this approach using molecular dynamics simulations of simple molecules in bulk with distinct dynamical characteristics with and without time scale separations as well as for inhomogeneous systems where a fluid is confined in a slit-like nanochannel. Additionally, we also apply our approach to more powerful many-body potentials optimized by using machine learning (ML).</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"10029-10040"},"PeriodicalIF":2.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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The Journal of Physical Chemistry A
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