The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce external fields centered on the solute to modulate the short-range repulsive interaction between the solute and solvent. This regularizes the binding energy distribution and makes it easy to calculate the free energy of the solute with the field. Together with the work done to apply the field in the presence and absence of the solute, we calculate the excess chemical potential of the solute. We present the formal development of this idea and apply it to study liquid water.
Accurate predictions of the hydration free energy for anions typically have been more challenging than for cations. Hydrogen bond donation to the anion in hydrated clusters such as $\mathrm{F(H_2O)}_n{}^-$ can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas-phase clusters shows that, even though anharmonic effects are interesting, they need not be troublesome magnitudes for careful appl…
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulati…
Using a neural network potential (ANI-1ccx) generated from quantum data on a large data set of molecules and pairs of molecules, isothermal, constant volume simulations demonstrate that the model can be as accurate as ab initio molecular dynamics for simulations of pure liquid water and the aqueous solvation of a methane molecule. No theoretical or experimental data for the liquid phase is used to train the model, suggesting that the ANI-1ccx approach is an effective method to link high level ab initio methods to potentials for large scale simulations.
用从头算分子动力学模拟方法对Na+水溶液进行了模拟.计算处理的Na+离子和32个水分子的周期性边界条件的立方体积确定的估计为零偏摩尔体积的水在正常密度和温度为344+/-24 K。12 ps轨迹的后半部分的分析显示，平均有4.6个水分子占据Na+离子的内部水化壳层，其中5个是最可能的占据。Na+的自扩散系数为1.0 x 10 $^{-5}$ cm $^2$ /s。溶液的准化学理论为另外两个计算提供了框架。首先，一个互补的计算，离子水簇的电子结构的结果和介电连续模型的外层水化贡献的基础上，预测平均水化壳占有率为4.0。这种低估是由于谐波近似的集群与近似的介电连续模型处理外球的贡献。最后，导致不敏感的复合自由能近似值的内球占位符的最大熵拟合表明，在这些条件下，Na+（aq）的水合自由能的值在-68千卡/摩尔附近，没有为填充或范德华相互作用提供贡献。
The lanthanide elements have well-documented similarities in their chemical behavior, which makes the valuable trivalent lanthanide cations (Ln(III)) particularly difficult to separate from each other in water. In this work, we apply ab initio molecular dynamics simulations to compare the free energies (Delta G(ads)) associated with the adsorption of lanthanide cations to silica surfaces at a pH condition where SiO- groups are present. The predicted Delta G(ads) for lutetium (Lu(III)) and europium (Eu(III)) are similar within statistical uncertainties; this is in qualitative agreement with our…
Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium K+ ion channels, and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distributi…
Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of $para$-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine-Learning (ML) based parametriza…
For the first time, an ab initio molecular dynamics simulation was performed to describe the C$_3$S/water interface. The simulation shows that oxides with favorable environment are protonated at first, creating very stable hydroxide groups. Proton transfers occur between water and silicates, and between water and hydroxides formed upon water dissociation on the surface. The typical lifetime of these events is on the same timescale than interconversion between Eigen and Zundel ions in bulk water. At the very early stage of the hydration encompassed by our simulation, silanol groups are very uns…
The hydration of ions in nanoscale hydrated clusters is ubiquitous and essential in many physical and chemical processes. Here we show that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO32- with n = 1-8 water molecules is investigated by ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically…
Predicting solvation free energies with an implicit solvent machine learning potential
Faculty of Physics and Center for NanoScience, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München（物理系和纳米科学中心、兽医学系，路德维希-马克西米利安大学慕尼黑）；Atomistic Modeling Center, Munich Data Science Institute, Technical University of Munich（原子模型中心、慕尼黑数据科学研究所，慕尼黑技术大学）；Multiscale Modeling of Fluid Materials, Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich（多尺度流体材料建模，工程物理与计算系，TUM工程与设计学院，慕尼黑技术大学）
In the context of nuclear fuel recycling and environmental issues, the understanding of the properties of radio-elements with various approaches remains a challenge regarding their dangerousness. Moreover, experimentally, it is imperative to work at sufficiently high concentrations to reach the sensitivities of the analysis tools, which often leads to precipitation for some of them, and stabilizing of specific oxidation states of some actinides remains a challenge, thus making it difficult to extract general trends across the actinide series. Complementary to experiments, modelling can be used…
