Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

A-form DNA is one of the biologically active double helical structure. The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology. In aqueous solution, the A-DNA structure will have a free transformation, the A-DNA structure will be translated into B-form structure with the evolution of time, and eventually stabilized in the B-DNA structure. To explore the stability function of the bivalent metal ions on the A-DNA structure, a series of molecular dynamics simulations have been performed on the A-DNA of sequence (CCCGGCCGGG). The results show that bivalent metal ions (Mg²⁺, Zn²⁺, Ca²⁺) generate a great effect on the structural stability of A-DNA in the environment of high concentration. As the interaction between metal ions and electronegative DNA chains, the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions. In metal salt solution with high concentration, metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure. Also, under the condition of the same concentration and valency of the metal ions, the stability of A-DNA structure is different. The calculations indicate that the structure of A-DNA in CaCl₂ solution is less stable than in MgCl₂ and ZnCl₂ solution.     

Free energy barrier for dissociation of the guanosine monophosphate anion in water

We report free energy barriers for the ground-state dissociation of the guanosinenucleotide anion in solution, employing implicit and explicit solvation models. The latterwas based on the Free Energy Perturbation technique and Monte Carlo simulations. For thelowest-energy structure, both solvation models indicate a solvent-induced transition froma dipole-bound state in the gas phase to a π^? valence state in solution. The freebarrier estimates obtained from explicit and implicit solvation are in fair agreement witheach other, although significantly overestimated in comparison to a previously reportedexplicit solvation model based on ab initio molecular dynamics simulations. Accounting forcorrections related to the different DFT functionals used in the present and previousstudies significantly improves the agreement.     

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe–ion direct correlation function and ion–ion dynamic structure factor. Although the power law decay is reminiscent of Debye–Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.     

Molecular dynamics simulations of a silver atom in water: evidence for a dipolar excitonic state

The properties of a silver atom in bulk water were studied for the first time by molecular dynamics simulations using two complementary mixed quantum-classical approaches. The first one consists of treating by quantum mechanics one electron only, which interacts with a classical silver cation and solvent through one-electron pseudopotentials. The second one is Car-Parrinello molecular dynamics that treats all the valence electrons quantum-mechanically. Very good agreement is obtained between these two methods, and the calculated absorption spectrum of the solvated silver atom agrees very well with experimental data. Both simulations reveal that the silver atom is in the critical region for the appearance of a dipolar excitonic state and exhibits a dipole moment of approximately 2 D with large fluctuations of +/-1 D. The structure of the solvation shell is also analyzed.     

The non-ideal solvation of NaCl in solvent: a simulation study

The non-ideality of the solvation of NaCl in a family of modified hybrid water solvent environments with varying local structural order is investigated using intensive molecular dynamics simulations. The results show that there are ion clusters of different size in all environments studied. The size distribution of the ion clusters is sensitive to the local structure of the solvent, which is determined by the hydrogen bonding strength. The ions are inclined to be in contact in solvents with high translational order, for competition between structure breaking among solvent molecules and structure formation around hydrated ions.     

Microscopic structure of liquid dimethyl sulphoxide and its electrolyte solutions: molecular dynamics simulations

Molecular dynamics (MD) simulations of pure dimethyl sulphoxide (DMSO) and solutions of Na⁺, Ca²⁺, Cl^?, NaCl and CaCl₂ in DMSO have been performed at 298.15 K and 398.15 K in NVT ensembles by using a four-interaction-site model of DMSO and reaction field method for Coulombic interactions. The structure of solvent, ion-solvation shells and ion-pairs have been analysed by employing a concept of coordination centres and characteristic vectors of the solvent molecule. Results are given for atom-atom (corresponding to DMSO), ion-atom and ion-ion radial distribution functions (RDFs), orientation of the DMSO molecules and their geometrical arrangements in the first solvation shells of the ions (Na⁺, Ca²⁺, Cl^?). A preferential formation of cyclic dimers with antiparallel alignment between dipole moments of nearest-neighbour molecules in the pure solvent is found. Geometrical models of the first coordination shells of the ions in ‘infinitely dilute solutions’ are proposed. Ion-ion RDFs in NaCl-DMSO and CaCl₂-DMSO solutions reveal the presence of both solvent separated (SSIP) and contact (CIP) ion pairs. The structures of the solvation shells of such ion pairs are also discussed.     

Permeation of ions through a model biological channel: effect of periodic boundary conditions and cell size

The effect of the simulation cell size and periodic boundary conditions on non-equilibrium molecular dynamics simulations of the structure and dynamics with explicit water molecules and ions in and near a model channel in a biological membrane is considered. The approach seems satisfactory. In particular, the presence of image channels that often contain image ions seems to have little effect on the average structure, channel content, or current for this system.     

Production of ultracold trapped molecular hydrogen ions

We have cooled ensembles of the molecular hydrogen ions H2+, H3+, and all their deuterated variants to temperatures of a few mK in a radio frequency trap, by sympathetic cooling with laser-cooled beryllium ions. The molecular ions are embedded in the central regions of Coulomb crystals. Mass spectroscopy and molecular dynamics simulations were used to accurately characterize the properties of the ultracold multispecies crystals. We demonstrate species-selective purification of multispecies ensembles. These molecules are of fundamental importance as the simplest of all molecules, and have the potential to be used for precision tests of molecular structure theory, tests of Lorentz invariance, and measurements of electron to nuclear mass ratios and their time variation.     

团簇分子[Zn-(CH_3CH_2OH)_n]~(2+)的荧光光谱研究及理论光谱验证

通过荧光光谱实验和理论计算对金属离子在乙醇溶液中的微团簇结构进行了研究。荧光光谱实验发现在275~330 nm范围存在较强的乙醇分子荧光峰,当加入盐离子(Zn~(2+))后该处荧光强度逐渐变弱,说明盐的加入对乙醇体系的荧光效率产生了影响,破坏了原有乙醇分子之间的作用,使得其刚性结构发生改变,荧光效率降低,同时Zn~(2+)与乙醇分子通过溶剂化作用形成了新的微团簇,在350~380 nm之间出现了新峰。通过对团簇结构[Zn-(H_2O)_n]~(2+)(n=1~3)进行优化比较,得到了相对精确及运算成本较低的密度泛函理论B3LYP方法,并应用于Zn~(2+)在乙醇溶液中团簇结构计算。结果表明体系的第一溶剂化层存在着n=1~6的微团簇分子,且最多为6。比较理论计算荧光光谱与实验荧光光谱,进一步说明了Zn~(2+)与乙醇形成了新的微团簇及计算方法的可行性。