氟化钙的分子动力学模拟——晶态、超离子态、熔融态和急冷非晶态

采用键序参数方法研究了Ca~(2+)亚晶格和F~-亚晶格,表明两者均可用键取向正态分布模型描述。超离子相Ca~(2+)亚晶格稳定地维持其原fcc结构,而F~-亚晶格表现为原sc结构的随机畸变。熔融相的模拟给出了实验上难以分离的三种径向分布函数。急冷非晶相的模拟表明体系是以Ca~(2+)离子为中心的等效球的无规密堆,由于Ca(2+)与其邻近的F~-离子没有形成某种确定的构形,体系不够稳定。     

熔融NaCaF3、Na2CaF4和Na3CaF5的分子动力学模拟

通过分子动力学模拟，研究了熔盐溶液NaCaF_3、Na_2CaF_4和Na_4CaF_5体系，模拟表明，三种二元混合系的径向分布函数十分接近．由模拟所得到的摩尔混合焓很好地与实验值一致．混合焓与Na~+离子势阱深度之间表现出很好的线性关系．模拟表明，在Na_2CaF_4体系中，即NaF-CaF_2二元系处于低共熔混合组分比NaF:CaF_2＝2:1时，Na~+，Ca~(2+)和F~-离子的自扩散系数出现很大的反常．     

单纯形法参量估算研究某些离子电极的非线性响应

本文用单纯形法由在线PC-1500袖珍计算机采集和处理数据,考察了Cl~-,F~-和Ca~(2+)电极的非线性响应。结果表明:引起Cl~-和Ca~(2+)电极的非线性响应是以电极活性材料的自身溶解为主,而F~-电极是由于干扰离子的影响所致。文中列出了三种电极活性材料的表观溶度积。本法可适用于其它离子选择性电极。     

大麦根细胞质膜存在H~+/Ca~(2+)反向传递系统

在发现大麦根细胞质膜上存在不需Mg~(2+)和需Mg~(2+)两个Ca~(2+)转运过程的基础上,进一步研究了这两个过程的转运机制,发现需Mg~(2+)的Ca~(2+)转运过程依赖于跨膜H~+梯度。无论以ATP为能源的、还是人为造成的跨膜H~+梯度,都可驱动跨膜Ca~(2+)转运;跨膜Ca~(2+)转运过程伴随着H~+梯度的消减。不需Mg~(2+)的转运过程则与跨膜H~+梯度无关。这些结果指出,大麦根细胞质膜上除了Ca~(2+)-ATP酶这一初级Ca~(2+)转运系统外,还存在一个以跨膜H~+梯度为能源的次级Ca~(2+)转运系统,即H~+/Ca~(2+)反向传递系统。     

分子动力学方法模拟不同温度下铀酰在叶腊石上的吸附和扩散行为

采用分子动力学方法研究了铀酰在叶腊石表面的吸附和扩散。在碳酸根离子存在的情况下,探究了温度对铀酰吸附和扩散的影响。碳酸根离子与铀酰存在较强的作用力,不同数目的碳酸根离子与铀酰结合会形成多种铀酰种态。在不同温度的模拟中,得到了UO_2~(2+)、UO_2CO_3、UO_2(CO_3)_2~(2-)、UO_2(CO_3)_3~(4-)四种铀酰种态和铀酰聚合物。通过原子密度图,观察了粒子在溶液中的分布情况。发现UO_2~(2+)+和UO_2CO_3容易吸附在叶腊石上,而UO_2(CO_3)_2~(2-)和UO_2(CO_3)_3~(4-)主要存在于扩散层中。随着时间的推移,越来越多的碳酸根离子与铀酰配位,使得铀酰在叶腊石上的吸附逐渐减少。本文计算了不同温度下,各铀酰种态的扩散系数。在扩散层中,各种态的扩散系数随温度的变化较为一致,而在吸附层中,UO_2~(2+)和UO_2CO_3的扩散速率随温度的变化较UO_2(CO_3)_2~(2-)和UO_2(CO_3)_3~(4-)慢。但是在同一温度下,同一个吸附层或扩散层中,铀酰种态的扩散系数大小顺序始终保持不变:UO_2~(2+)UO_2CO_3UO_2(CO_3)_2~(2-)UO_2(CO_3)_3~(4-)。说明在碳酸根存在的情况下,UO_2~(2+)可能是主要的扩散形式。     

跨膜Ca~(2+)梯度通过磷脂酰胆碱调节肌质网Ca~(2+)-ATP酶

将纯化的肌质网Ca~(2+)-ATP酶重组在具有或不具有跨膜Ca~(2+)梯度的脂质体上,研究了磷脂(特别是磷脂酰胆碱)在跨膜Ca~(2+)梯度对肌质网Ca~(2+)-ATP酶功能调节中的作用。结果表明:(1)高浓度的(Ca~(2+)对与不同磷脂保温的去脂Ca~(2+)-ATP酶都产生抑制,但对与PC保温的Ca~(2+)-ATP酶抑制最大。(2)当存在一个正向跨膜Ca~(2+)梯度时(酶活性中心一侧Ca~(2+)浓度较低,类似生理条件),它只对与中性磷脂PC:PE重组的Ca~(2+)-ATP酶产生抑制,且PC:PE(摩尔比)为1:1时,抑制程度最大。如以酸性磷脂PS或PG替代PC则均无明显抑制。(3)比较不同脂肪酸侧链的PC的作用表明,当DOPC或DPPC存在时均有明显抑制作用,而DMPC则几乎不表现抑制作用。(4)若Ca~(2+)梯度逆转,则无论是与酸性磷脂或中性磷脂重组的肌质网Ca~(2+)-ATP酶都会被抑制。     

肺Ca2+含量与硅肺的关系

本文用离子选择电极测定了实验性诱发硅肺大鼠的肺、脑、肾、肝和血清中的[Ca~(2+)]、[K~+]和[Na~+],还以荧光探针Tb~(3+)探讨了Ca~(2+)的作用。在硅肺形成后,大鼠的肺、脑、肾、肝和血清等组织中的游离[Ca~(2+)]均发生变化。荧光探针表明:硅肺大鼠肺Ca~(2+)增加部分来自线粒体Ca~(2+)的释放硅肺。大鼠肺中游离Ca~(2+)和线粒体Ca~(2+)的变化可能与巨噬细胞的损伤有关。     

希土化合物的药理学作用

目前,尽管还没有发现希土元素参与了任何一个天然生物学过程,但大量实验事实说明,希土离子和许多生物大分子都有程度不同的亲合力,对多种酶或酶原具有激活或抑制作用。尤其希土离子与在人体内起重要作用的Ca~(2+)离子十分相似,而电荷密度又比Ca~(2+)高,因此能取代Ca~(2+)离子,参予与Ca~(2+)有关的许多生理过程。希土离子的这种性质,一方面由于它     

MCM-22型分子筛中苯分子吸附行为的分子动力学模拟

用分子动力学方法研究了纯硅ＭＣＭ－２２型分子筛中苯分子的吸附行为。计算结果表明,模拟采用刚性骨架或柔性骨架对苯分子的扩散系数并没有大的差别,这表明在较低吸附值的情况下,分子筛骨架的柔性对苯分子吸附和扩散并没有产生大的影响。     

熔融ZnCl2结构的分子动力学模拟研究

熔融ZnCl2作为一种离子性共价性参半的典型熔盐, 其近邻结构在实验测量和分子动力学模拟方面均作过一些研究。本文依据新近EXAFS实验结果, 比较了不同的有效势下模拟得到的径向分布函数,表明KDR势可作为一种实用势。并进一步在KDR势模拟产生的瞬态构型基础上, 使用键序参数方法研究了晶态和熔融态ZnCl2中的近邻结构。结果表明, 和晶态ZnCl2一样, 在熔融ZnCl2中存在稳定的Zn/Cl正四面体结构, 但熔态和晶态Zn/Cl近邻结构热波方差σ不同。计算表明300K晶态σ=5.0℃, 613K熔融态σ=12.2℃。也对熔融ZnCl2的网络状结构和宏观输运性质进行了讨论。     

分子动力学模拟研究熔盐中的局部结构

我们用分子动力学(MD)方法通过计算机模拟研究了熔盐中的键取向序和局部结构。描述局部结构的简单方法是计算键角分布几率,但它不能给出键取向序的三维空间描述。有的文献采用Direchlet-Voroitol(DV)多面体处理MD模拟产生的瞬态构型,但DV     

分子动力学模拟研究LiCl急冷非晶形成过程中的局部结构

The local structure of quenching process of lithium chloride has been studied by molecular dynamics simulation. The sequentially-quenched model was adapted. When the equilibrium reached at the melting point 878 K, the system was fastly quenched to 698 K and then the system relaxed to equilibrium. The process was repeated as above and the system was quenched to 498 K, 298 K, and 198 K, respectively, We calculated the quadratic invariants Q_l histograms at different temperatures by averaging the Q_l values of theinstantaneous configurations with the method of fond spherical harmonics statistics under equal neighbor number. Consulting the Q_l histograms of the linear combination model with a parameter of square deviation in which model the local diamond structure was predominant, we found that the Q_l histograms from the model and those from the simulation were very similar. The results showed that in the quenched LiCl system the local orientation obviously tended to be binary diamond structure (like GaAs) and the square deviation in model would be decreased with the lowering of simulation temperature.     

Potential energy surfaces and dynamics of Ni2+ ion aqueous solution: molecular dynamics simulation of the electronic absorption spectrum

We develop a model effective Hamiltonian for describing the electronic structures of first-row transition metals in aqueous solutions using a quasidegenerate perturbation theory. All the states consisting of 3d(n) electronic configurations are determined by diagonalizing a small effective Hamiltonian matrix, where various intermolecular interaction terms such as the electrostatic, polarization, exchange, charge transfer, and three-body interactions are effectively incorporated. This model Hamiltonian is applied to constructing the ground and triplet excited states potential energy functions of Ni(2+) in aqueous solution, based on the ab initio multiconfiguration quasidegenerate perturbation theory calculations. We perform molecular dynamics simulation calculations for the ground state of Ni(2+) aqueous solution to calculate the electronic absorption spectral shape as well as the ground state properties. Agreement between the simulation and experimental spectra is satisfactory, indicating that the present model can well describe the Ni(2+) excited state potential surfaces in aqueous solution.     

Molecular dynamics simulation of surface segregation in a (110) B2-NiAl thin film

Surface segregation in (110) B2-NiAl film approximately 3 nm thick is investigated by using molecular dynamics simulation with a reliable embedded-atom potential. The simulation is performed for the stoichiometric composition at a temperature of 1500 K, just below the melting temperature of the film model. It is found that the (110) surface is structurally stable but develops adatoms, vacancies and antisites. The coverage of an adatom layer is estimated to be ～0.07 ML (monatomic layers) and it contains on average ～95% of Al atoms. The top (surface) and second (subsurface) layers of the (110) surface is the most enriched in Ni relative to the bulk composition. These layers contain on average ～51% of Ni atoms. The Ni fraction in the third and forth layers of the film is estimated as ～50.5%. The deeper layers have essentially the bulk composition. Vacancies in the film model are found only on the Ni sublattice. The vacancy concentration on the Ni sublattice in the top layer is ～7.5%. The second layer almost does not contain vacancies. The next layers have essentially the constant bulk vacancy composition which can be estimated as ～1.3-1.4%.     

A model electronic Hamiltonian to study low-lying electronic states of [Fe(bpy)3]2+ in aqueous solution

A simple model electronic Hamiltonian to describe the potential energy surfaces of several low-lying d-d states of the [Fe(bpy)(3)](2+) complex is developed for use in molecular dynamics (MD) simulation studies. On the basis of a method proposed previously for first-row transition metal ions in aqueous solution, the model Hamiltonian is constructed using density functional theory calculations for the lowest singlet and quintet states. MD simulations are then carried out for the two spin states in aqueous solution in order to examine the performance of the model Hamiltonian. The simulation results indicate that the present model electronic Hamiltonian reasonably describes the potential energy surfaces of the two spin states of the aqueous [Fe(bpy)(3)](2+) system, while retaining sufficient simplicity for application in simulation studies on excited state dynamics.     

Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution

Structural and dynamical properties of the TiO(2+) ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent-solvent interactions. Both first and second hydration shell have been treated at Hartree-Fock (HF) quantum mechanical level. A Ti-O bond distance of 1.5 A was observed for the [Ti=O](2+) ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 A and 2.1 A, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO(2+) hydrate can be characterized as [(H(2)O)(0.7)(H(2)O)(4) (eq)(H(2)O)(ax)](2+). The second shell consists in average of 12 water molecules located at a mean distance of 4.4 A. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO(2+) ion in aqueous solution. For the dynamics of the TiO(2+) ion, different sets of dynamical parameters such as Ti=O, Ti-O(eq), and Ti-O(ax) stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps.     

Insights into the structure and dynamics of a room-temperature ionic liquid: ab initio molecular dynamics simulation studies of 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]-CO2 mixture

Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.     

On the solvation of the Zn2+ ion in methanol: a combined quantum mechanics, molecular dynamics, and EXAFS approach

The solvation properties of the Zn(2+) ion in methanol solution have been investigated using a combined approach based on molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) experimental results. The quantum mechanical potential energy surface for the interaction of the Zn(2+) ion with a methanol molecule has been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective Zn-methanol interactions have been fitted by suitable analytical potentials, and have been utilized in the MD simulation to obtain the structural properties of the solution. The reliability of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to the EXAFS experiments.     

Molecular dynamics extended for fluctuating networks: Application to water

Molecular simulation models are increasingly important tools in efforts to understand the role that water plays in biochemical processes. However, existing models of water have limited capacity to deal with the characteristics of hydrogen bond networks. This article proposes a new fluctuating network (FN) algorithm as an extension of the standard molecular dynamics algorithm. The new algorithm allows for the simulation of a molecular system based on an underlying network, such as the hydrogen bond network in water. This algorithm distinguishes strong from weak network connections, applying a potential that best describes the specific connection behavior. We model liquid water with this new technique using a single‐site, isotropic, short‐range potential. We successfully reproduce liquid water's signature molecular spacing (as represented by the radial distribution function) and characterize its dynamic properties including the exponential hydrogen bond lifetime distribution, diffusion rate, and average hydrogen bonds per molecule. The FN algorithm allows exploration of the behavior of networked systems where explicit coordination limits are required. As such it could also be used to model covalent interactions, reaction dynamics, and applied to simulation of cellular networks. © 2012 Wiley Periodicals, Inc.     

Use of molecular dynamics simulations with ab initio SCF calculations for the determination of the deuterium quadrupole coupling constant in liquid water and bond lengths in ice

The deuterium quadrupole coupling constant and asymmetry parameter in heavy water were determined using ab initio SCF calculations. Snapshots from a molecular dynamics simulation were used to give liquid water cluster configurations and the influence of simulation parameters on the quadrupole coupling constant was investigated. The electronic potential model and the number of molecules in the molecular dynamics simulation and the pressure of the system were found to have only a small influence on the quadrupole coupling constant. The average value of the quadrupole coupling constant at room temperature, corrected for the known deficiency of the ab initio calculation in the gas phase, yields a quadrupole coupling constant of 253 kHz, in perfect agreement with the most recent experiments. The oxygen—deuterium bond lengths in ice Ih, ice II, and ice IX were determined using experimental quadrupole coupling constants and a model equation. An averaged bond length of 98.9 pm was obtained for the Ih form, which is approximately 2 pm shorter than that determined by neutron diffraction studies, whereas the bond lengths for the four deuterium sites in ice II and the three sites in ice IX are in fair agreement with experiment. © John Wiley & Sons, Inc.