镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估

doi:10.3866/PKU.WHXB201908035

物理化学学报 >> 2020, Vol. 36 >> Issue (11): 1908035.doi: 10.3866/PKU.WHXB201908035

镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估

刘子义¹^,², 夏苗仁¹^,², 柴之芳¹^,³, 王东琪¹^,*()

¹ 中国科学院高能物理研究所多学科中心, 北京 100049
² 中国科学院大学化学学院, 北京 100049
³ 苏州大学放射医学与辐射防护国家重点实验室, 苏州大学放射医学与防护学院, 江苏苏州 215123

收稿日期:2019-08-29 录用日期:2019-09-24 发布日期:2019-09-29
通讯作者: 王东琪 E-mail:dwang@ihep.ac.cn
基金资助:
国家自然科学基金(91026000);国家自然科学基金(21473206);国家自然科学基金(91226105);中国科学院百人计划项目(Y2291810S3)

Parameterization and Validation of AMBER Force Field for Np⁴⁺, Am³⁺, and Cm³⁺

Ziyi Liu¹^,², Miaoren Xia¹^,², Zhifang Chai¹^,³, Dongqi Wang¹^,*()

¹ Multidisciplinary Initiative Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China
² University of Chinese Academy of Sciences, Beijing 100049, P. R. China
³ State Key Laboratory of Radiation Medicine and Protection, and School of Radiation Medicine and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, Jiangsu Province, P. R. China

Received:2019-08-29 Accepted:2019-09-24 Published:2019-09-29
Contact: Dongqi Wang E-mail:dwang@ihep.ac.cn
Supported by:
the National Natural Science Foundation of China(91026000);the National Natural Science Foundation of China(21473206);the National Natural Science Foundation of China(91226105);CAS Hundred Talents Program(Y2291810S3)

摘要/Abstract

摘要：

：锕系元素具有高放射性和毒性，为开展锕系水溶液化学的实验研究带来了困难与挑战。得益于理论计算方法和计算能力的快速发展，运用分子动力学模拟水溶液环境并研究锕系在水溶液当中的化学行为成为一种可替代的方法。本文拟合了Np⁴⁺、Am³⁺、Cm³⁺三种金属离子的力场参数并进行了评估，进而将其用于溶液配位化学和动力学研究。为了研究的系统性，也开展了Th⁴⁺、U⁴⁺、Pu⁴⁺三种锕系离子的分子模拟研究。基于对上述六种离子的分子动力学研究，系统报道了该六种锕系离子的第一、二溶剂化层结构、性质、立体化学及驻留时间等方面的共性与特性，并从能量方面探究这些内在差异的原因。结果显示，本文报道的参数适用于锕系离子的配位结构和结合自由能的研究，但对于动力学性质的研究，宜谨慎用于相同价态的锕系离子溶液体系的定性理解。本文也探究了六种锕系离子在水溶液中与Cl^-、NO₃^-和CO₃^2-的相互作用，分析了各配合物配位模式、成键规律及结合强弱。综上所述，本项工作发展了三种关键锕系离子的力场参数，有助于开展基于AMBER力场的动力学方法的An^3+/4+溶液化学的研究，丰富了对An^3+/4+的水溶液中配位化学的认识。

关键词: An³⁺, An⁴⁺, AMBER力场

Abstract:

The radioactivity and toxicity of actinides impede experimental investigation into their chemical properties in the condensed phase. The rapid development of computational methods and computational facilities allows for alternative experimental methods, including the use of a molecular force field, to gain insight into the coordination chemistry and dynamics of actinides. The key to this method is the force fieild parameters. In the present work, we report the development and validation of the AMBER (Assisted Model Building with Energy Refinement) force field parameters for Np⁴⁺, Am³⁺, and Cm³⁺ based on the experimentally determined ion-oxygen distance (IOD). The parameter set, together with that reported for Th⁴⁺, U⁴⁺, and Pu⁴⁺, was then applied to investigate the coordination chemistry and dynamics of these six actinide ions in the aqueous phase, in the absence and presence of counterions Cl^-, NO₃^-, and CO₃^2-. The simulations showed a shorter An-O_w coordination length for An⁴⁺ than for An³⁺, and for higher atomic numbers of ions in the same valence state. Th⁴⁺ preferentially existed in a 10-coordinated state, adopting a BCASP (bicapped square antiprism) conformation, while the other ions tended to be 9-coordinated with a CASP (capped square antiprism) conformation. The only exception was Cm³⁺, which adopted a TCTP (tricapped trigonal prism) conformation. The results also showed that the water molecules around An⁴⁺ were more ordered than those around An³⁺, as indicated by the smaller angles between the An-O_w vector and the dipole direction of the water ligand. This highly ordered structure of coordinated water affected their translation and rotation, i.e., the diffusion coefficient and rotational relaxation time of the water molecules around An⁴⁺ were smaller than those in the case of An³⁺ due to the stronger electrostatic interaction between An⁴⁺ and ligating water. The hydration free energies of the targeted actinide ions were also calculated by the FEP (free energy perturbation) method. An⁴⁺ underwent a greater degree of stabilization than did An³⁺ upon hydration; among the ions in the same oxidation states, those with a higher atomic number were better stabilized. In summary, the results of the simulations were consistent with the literature data in terms of the hydration structure, coordination of counterions, and hydration free energy of the actinide ions. The ability of the parameter set to describe the dynamics of water in the vicinity of actinides remains to be verified due to the lack of reference data. We tentatively propose that it may be used to investigate the coordination chemistry of actinides both in conformational analysis and binding strength, while special care should be taken when studying the kinetics of the solvated system. This work is expected to enrich our understanding of the solution behavior of An³⁺/An⁴⁺ at the force field level.

Key words: An³⁺, An⁴⁺, AMBER force field

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刘子义, 夏苗仁, 柴之芳, 王东琪. 镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估[J]. 物理化学学报, 2020, 36(11): 1908035.

Ziyi Liu, Miaoren Xia, Zhifang Chai, Dongqi Wang. Parameterization and Validation of AMBER Force Field for Np⁴⁺, Am³⁺, and Cm³⁺[J]. Acta Physico-Chimica Sinica, 2020, 36(11): 1908035.

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201908035

https://www.whxb.pku.edu.cn/CN/Y2020/V36/I11/1908035

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	IOD/nm	(R/2)/nm	ε/(kJ·mol^?1)
Am³⁺	0.248	0.1688	0.545091
Cm³⁺	0.246	0.1673	0.504702
Th⁴⁺	0.245	0.1713	0.615900
U⁴⁺	0.242	0.1689	0.547840
Np⁴⁺	0.240	0.1673	0.504702
Pu⁴⁺	0.239	0.1666	0.486411

		First hydration shell		Second hydration shell
		D	CN	d	CN
Th⁴⁺	this work	0.243	9.9	0.451	17.7
Th⁴⁺	Ref.	0.245 ⁴¹	9–10 ⁴¹	0.466 ^{10, 45, 48}	18 ^{10, 45, 48}
U⁴⁺	this work	0.239	9.1	0.445	17.6
U⁴⁺	Ref.	0.242 ⁴¹	9–10 ⁴¹	–	–
Np⁴⁺	this work	0.239	9	0.443	17
Np⁴⁺	Ref.	0.240 ²⁰	8–10 ⁴⁹	–	–
Pu⁴⁺	this work	0.237	9	0.443	17.4
Pu⁴⁺	Ref.	0.239 ⁴³	8 ⁴³	–	–
Am³⁺	this work	0.248	9	0.460	16
Am³⁺	Ref.	0.248 ²⁴	9 ⁴⁹	0.464 ⁵⁰	21.2 ⁵⁰
Cm³⁺	this work	0.246	9	0.456	16
Cm³⁺	Ref.	0.246 ²⁴	9 ⁴⁹	0.462 ¹²	15.8 ⁴⁷

		Th⁴⁺	U⁴⁺	Np⁴⁺	Pu⁴⁺	Am³⁺	Cm³⁺
D_An	this work	0.67	0.35	0.36	0.51	0.38	0.46
D_An	Ref.					0.62 ⁵¹	0.61⁵¹
D_wat	this work	0.52	0.48	0.45	0.45	0.50	0.51
τ	this work	9.36	10.03	10.19	10.42	7.35	7.31
τ_r	this work	0.19	0.27	0.50	0.83	18.2	~34 ns
τ_r	Ref.	< 20 ns ⁵²	182 ns ⁵²	–	–	tens of ns ⁵²	tens of ns ⁵²
ΔG	this work	4.2	4.4	4.8	5.1	6.9	7.3
ΔG	Ref.	6.9	8.3	–	–	> 6.5	> 6.5

	ΔG_(FEP)	ΔG_(CORR)	ΔG ⁵⁶	ΔG ⁵⁷	ΔG ⁵⁸	ΔG ⁵⁹
Th⁴⁺	?5101.16 ± 0.78	?6072.9	–	–	?6104.1	?5818.8
U⁴⁺	?5157.47 ± 0.74	?6139.9	–	–	?6305.2	?6564.4
Np⁴⁺	?5188.70 ± 0.53	?6177	–	?6161.1	?6498.3	–
Pu⁴⁺	?5208.09 ± 0.81	?6200.1	–	–	?6448.3	?6364.4
Am³⁺	?2982.47 ± 0.77	?3277.4	?3299.6	?3200.1	?3161.1	–
Cm³⁺	?3022.16 ± 0.69	?3321.1	?3328.5	?3257.2	?3227.1	–

	Cl^?		NO₃^? (O coordinated)		CO₃^2?(O coordinated)
	this work	Ref.	this work	Ref.	this work	Ref.
Th⁴⁺	0.270(9.3)	0.272(10) ⁶⁰	0.230(9.2)	0.258(12)⁶⁴	0.229(9.7)	0.250(10) ⁶⁷
U⁴⁺	0.267(9)	0.263(6.0) ⁶¹	0.227(9)	0.253(12) ⁶⁵	0.226(9)	0.249(10) ⁶⁸
Np⁴⁺	0.266(9)	0.269(9.9) ²⁰	0.226(9)	0.252(11.5) ²¹	0.223(9)	0.244(10) ⁶⁶
Pu⁴⁺	0.264(9)	0.262(8) ⁶⁰	0.224(9)	0.239(10) ⁶⁰	0.221(9)	0.242(10) ⁶⁹
Am³⁺	0.281(8.8)	0.280(8.8) ²⁴	0.242(8.8)	0.255(10) ⁶³	0.232(9)	–
Cm³⁺	0.275(8.8)	0.276(8.7) ²⁴	0.240(8.8)	0.251(10) ⁶³	0.230(9)	0.234–0.2419(9) ⁵⁰

镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估

Parameterization and Validation of AMBER Force Field for Np⁴⁺, Am³⁺, and Cm³⁺

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	Cl^?		NO₃^?		CO₃^2?
	ΔG₁	ΔG_bind	ΔG₁	ΔG_bind	ΔG₁	ΔG_bind
Am³⁺	?380.2 ± 0.29	?0.84	?394.8 ± 0.27	?24.7	?1552.9 ± 0.59	?136.1
Cm³⁺	?371.0 ± 0.29	0.4	?399.4 ± 0.31	?28.9	?1544.9 ± 0.61	?128.1
Th⁴⁺	?370.1 ± 0.32	1.3	?411.6 ± 0.26	?41.4	?1671.4 ± 0.52	?254.6
U⁴⁺	?417.0 ± 0.28	?45.2	?428.3 ± 0.28	?58.2	?1671.4 ± 0.48	?254.6
Np⁴⁺	?417.8 ± 0.23	?46.5	?427.9 ± 0.33	?57.8	?1676.4 ± 0.44	?259.6
Pu⁴⁺	?410.3 ± 0.26	?38.9	?425.4 ± 0.25	?55.3	?1692.3 ± 0.52	?275.5

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镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估

Parameterization and Validation of AMBER Force Field for Np4+, Am3+, and Cm3+

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Parameterization and Validation of AMBER Force Field for Np⁴⁺, Am³⁺, and Cm³⁺