Equilibrium properties of a hysteresis dimer molecule from MD simulations using two-body potentials

Recent experiments indicate that electromagnetic hysteresis behavior can be exhibited at the molecular level. Based on these indications, a simple dimeric molecule with a hysteresis-like pathway with diﬀerent spatial coordinates for formation and break-up is described and a MD simulation using 2-body potentials and switches to form and break bonds is implemented to determine whether chemical reaction pathways might also exhibit analogous behavior whilst preserving conventional thermodynamical outcomes. The results of various common thermodynamical and kinetic properties are presented, where no unusual thermodynamics is observed for the chemical reaction with the loop pathway which might be interpreted as not being ”‘time reversible invariant”’ and therefore susceptible to manifesting unusual thermodynamical phenomena. This system may well model particles that interact via the electro-magnetic ﬁeld to form molecules, since hysteresis behavior is standard and well rep-resented in large-scale magnetic and electrical systems, especially in the solid state. The potential switching technique circumvents the problem of computer intensive three-body calculations which makes this model particularly suitable for numerical investigations in both equilibrium and nonequilibrium states where the details of a particular reaction mechanism and its reaction coordinates are not the focus of attention. A new algorithm for the conservation of energy and momentum is incorporated in regions where the potentials are switched. The thermodynamical parameters determined include the standard free energy, enthalpy and entropy, the activity coeﬃcient ratios, the equilibrium constant and the many energy distribution functions of the molecule, all of which are compared to the Maxwell distribution function.Both the free dimer and atom particle kinetic energy distributions agree fully with Maxwell-Boltzmann statistics but the distribution for the relative kinetic energy of bonded atoms does not, thereby opening to question recent far-from-equilibrium theories such as MNET that make use of this presupposition in a fundamental sense. The kinetic parameters determined include the rotational and translational diﬀusion coeﬃcients and the Arrhenius parameters. Most applications of rotational diﬀusion seem to presuppose a projection of a value about the rotational axis (leading to a cosine dependence) but here it is shown that an angular dependence is also a feasible model during a ﬁrst order relaxation process. An NEMD simulation which uses a novel diﬀerence equation to test for mass conservation is presented which shows numerically that the principle of local equilibrium (PLE) is violated and is at best only an approximation. The results suggest that although the reaction is microscopically loop-like, unlike all the models routinely proposed, yet the thermodynamics is entirely ”‘normal”’ and yields results that do not contradict any of the known laws of thermodynamics. It is therefore postulated that reaction dynamics involving hysteresis mechanisms can occur in nature and may be experimentally veriﬁable, although experimental interpretations tend to construct models that avoid such mechanisms. A revision of the concept of ”‘time reversibility”’ to accom-modate the above results is suggested. The general design of the reaction mechanism also allows for the use of conventional potentials without hysteresis and this will be the object of future investigation.