SHENG Nan

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

University of the Chinese Academy of Sciences, Beijing 100049, China, E-mail: shengnan@sinap.ac.cn TU Yu-song

Institute of Systems Biology, Shanghai University, Shanghai 200444, China

GUO Pan

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

University of the Chinese Academy of Sciences, Beijing 100049, China

WAN Rong-zheng, FANG Hai-ping

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

(Received November 8, 2012, Revised November 10, 2012)

DIFFUSING OF AN AMMONIA MOLECULE IN WATER IN A VERY SHORT TIME PERIOD*

SHENG Nan

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

University of the Chinese Academy of Sciences, Beijing 100049, China, E-mail: shengnan@sinap.ac.cn TU Yu-song

Institute of Systems Biology, Shanghai University, Shanghai 200444, China

GUO Pan

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

University of the Chinese Academy of Sciences, Beijing 100049, China

WAN Rong-zheng, FANG Hai-ping

Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China

(Received November 8, 2012, Revised November 10, 2012)

The diffusion of an ammonia molecule (NH3) in water was investigated by molecular dynamic simulations. It is found that the diffusion shows negative correlation with its dipole orientation.

diffusion, ammonia, correlation

Introduction

The investigated system includes 2 178 water molecules together with an ammonia molecule (NH3) in a box with the initial size of 4.0 nm × 4.0 nm × 4.0 nm. We used the Optimized Potentials for Liquid Simulations (OPLS)[1]force field and SPC/E water model in simulations. Periodic boundary conditions were imposed in all dimensions and the particle mesh Ewald method[2]was employed for full electrostatics. After 2 ns simulation for equilibrium, a 120 ns simulation under NVT ensemble was taken for analysis with a time step of 1 fs. The molecular dynamics simulations were performed with the Nosé-hoover thermostat[3,4](300 K) using the software Gromacs 4.5[5].

Figure 1 shows the drifts Sdriftof the diffusingdisplacements in the direction of the ammonia dipole for different time intervals, which are the mean values of the projections of the diffusing displacements in the dipole direction of the ammonia molecule, defined as

where r(t) is the coordinates of the ammonia molecule at time t and(t ) is the unit vector in the dipole direction of the ammonia molecule at time t. We can see that the drift is very small as Δt is close to zero. The drift arises very fast as Δt ≤10ps. In the range of 10ps <Δt ≤300ps, the drift increases slowly and reaches a peak value of -0.056 nm at Δt=300ps. This shows that the diffusing displacements of the ammonia molecule in the time interval of 300 ps have a mean drift of 0.056 nm in the opposite direction of the ammonia dipole. Then the drift decreases as Δt＞300ps. When the time interval is larger than 800 ps, the drift approaches zero, indicating that the diffusion is no longer correlated with the dipole direction.

Fig.1 Drifts of the diffusing displacements in the direction of the ammonia dipole with respect to time interval (The error bars are the confidence intervals for mean value at a confidence level of 95%). Inset shows an ammonia molecule which has a trigonal pyramidal shape (one nitrogen on top and three hydrogen on bottom) with a bond angle of 107.8o. The molecule has a dipole due to this asymmetric structure of nitrogen and hydrogen

Fig.2 Directional correlation between the diffusing displacement and the dipole of the ammonia molecule with respect to time interval (The error bars are the confidence intervals for mean value at a confidence level of 95%).

The asymmetrical structure of the drift manifests that the ammonia molecule “l(fā)ikes” diffusing larger distance in the direction opposite to its dipole direction than in other directions. The reason for such a drift contribution is the directional correlation between the diffusing displacement and the ammonia dipole. The directional correlation is defined in Eq.(2) and illustrated in Fig.2.

The correlation time between dipole direction and diffusing displacement is comparable to the autocorrelation time for water from MD simulations[6], and the drifts of the diffusing displacements in the direction of the ammonia dipole is consistent to the biased motion of the asymmetric molecules with a fixed asymmetric axis as that observed in a nanotube[7].

We believe that the asymmetric behavior can also be found for the other molecules with asymmetrical structure and charges. This is different from the conventional view that the diffusion of a molecule or nanoscale item by the thermal fluctuations is symmetric. More importantly, the correlation time and the quantity of the biased diffusion can be large for large molecules (items) due to the inertia effect. We expect that this is of particular importance for the biological systems as well as the cosmo-systems and our finding can be the base of the statistical physics in the nanoscale systems. We note that we did not consider the partial hydrolyzation of ammonia molecule in simulations. This does not change our conclusion of the asymmetric molecule diffusion at nanoscale as we focus on the diffusion behavior of an asymmetrical molecule at very short time periods.

Acknowledgement

The authors acknowledge the Shanghai Supercomputer Center of China.

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10.1016/S1001-6058(11)60325-9

* Project supported by the National Natural Science Foundation of China (Grant Nos. 10825520, 11175230).

Biography: SHENG Nan (1987-), Male, Ph. D. Candidate

FANG Hai-ping,

E-mail: fanghaiping@sinap.ac.cn