Molecular behavior and ring closure dynamicsof n-alkane chain in solution

Abstract

The molecular dynamics method was applied for the behavior of a n-alkane chain in solution. The model of the chain molecule is a semi-rigid one, i.e., bond length and bond angle are fixed, and the rotation angle is changed with the rotational potential. We calculated the equilibrium properties of the system, e.g., the pair correlation functions between the chain element and solvent molecules $g_{sc}$(r), and between the chain elements $g_{cc}$(r), and the fraction of the conformers $X_Φ$ with bond rotation angle $\phi$, and the configurational properties such as the mean square end-to-end distance $<R^2>$, and the mean square radius of gyration $<S^2>$. We also obtained the dynamic properties of the system, e.g., the autocorrelation function C(A;t) where $A=R^2(t)$, $S^2(t)$, $\stackrel{R}{\sim}(t)$ or $\stackrel{V}{\sim}(t)$, and the diffusion constant D. We studied the effect of the temperature T, rotational potential barrier $V_m$ and the number of chain element $N_c$ on the behavior of the chain molecule. The $g_{sc}$(r) is dependent on T but independent of $V_m$ or $N_c$; the $g_{CC}(r)$ is, however, dependent on T or $V_m$ and independent of $N_c$; the configurational properties $<R^2>$ and $<S^2>$ increase as T, $V_m$ and $N_c$ increase. The $C(R^2;t)$ and $C(S^2;t)$ relax faster as decreasing T or $N_c$ and increasing $V_m$ whereas $C(\stackrel{V}{\sim};t)$ of the center of mass relaxes faster when T, $V_m$ and $N_c$ decrease. And D increases with increasing T and $V_m$ but decreases with increasing $N_c$. The $C(\stackrel{V}{\sim};t)$ of the end point of chain relaxes nearly equal since the chain at the end point has less constraint. The effects of T are explained with the relation of the interaction between chain and solvent molecules and the translational motion of the particle. The $V_m$ effects are discussed by the intramolecular interaction between chain elements. And the $N_c$ effects are related with the chain dimension. And we studied the ri...