Molecular dynamics temperature/pressure dependence

The general experimental approach used in 2D correlation spectroscopy is based on the detection of dynamic variations of spectroscopic signals induced by an external perturbation (Figure 7.43). Various molecular-level excitations may be induced by electrical, thermal, magnetic, chemical, acoustic, or mechanical stimulations. The effect of perturbation-induced changes in the local molecular environment may be manifested by time-dependent fluctuations of various spectra representing the system. Such transient fluctuations of spectra are referred to as dynamic spectra of the system. Apart from time, other physical variables in a generalised 2D correlation analysis may be temperature, pressure, age, composition, or even concentration. 

It is also evident that this phenomenological approach to transport processes leads to the conclusion that fluids should behave in the fashion that we have called Newtonian, which does not account for the occurrence of non-Newtonian behavior, which is quite common. This is because the phenomenological laws inherently assume that the molecular transport coefficients depend only upon the thermodyamic state of the material (i.e., temperature, pressure, and density) but not upon its dynamic state, i.e., the state of stress or deformation. This assumption is not valid for fluids of complex structure, e.g., non-Newtonian fluids, as we shall illustrate in subsequent chapters. 

The computational efficiency of a FF approach also enables simulations of dynamical behavior—molecular dynamics (MD). In MD, the classical equations of motion for a system of N atoms are solved to generate a search in phase space, or trajectory, under specified thermodynamic conditions (e.g., constant temperature or constant pressure). The trajectory provides configurational and momentum information for each atom from which thermodynamic properties such as the free energy, or time-dependent properties such as diffusion coefficients, can be calculated. 

Tinte et al.54 have carried out molecular dynamic simulations of first-principles based effective Hamiltonian for PSN under pressure and of PMN at ambient pressure that clearly exhibit a relaxor state in the paraelectric phase. Analysis of the short-to-medium range polar order allows them to locate Burns temperature Tb. Burns temperature is identified as the temperature below which dynamic nanoscale polar clusters form. Below TB, the relaxor state characterized by enhanced short-to-medium range polar order (PNR) pinned to nanoscale chemically ordered regions. The calculated temperature-pressure phase diagram of PSN demonstrates that the stability of the relaxor state depends on a delicate balance between the energetics that stabilize normal ferroelectricity and the average strength of quenched "random" local fields. 

As in standard molecular dynamic simulations, the box is gradually heated, i.e., velocities of the atoms are increased, and eventually the size of the box is scaled up or down to the conditions of interest (pressure and temperature). In contrast to standard simulations, the present one is stopped periodically to perform DFT calculations on a small sample of the box. This is basically done to obtain new charges but eventually it can be modified to obtain new geometric parameters and force constants, depending on the specific properties that are target of the calculations. This procedure continues during heating principally and at the initial part of equilibration until a self-consistent force field compatible with the real conditions, is obtained for the equilibrated box. 

Tsolou, G., Harmandaris, V.A., and Mavrantzas, V.G. (2006) Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cz5-1,4-polybutadiene, J. Chem. Phys. 124, 084906... 

The p-T phase diagram of sulfur is about the most complicated amongst the chemicd elements, and many open questions still exist with respect to phase boundaries, structures in detail, and kinetics of phase transitions in the solid as well as in the hquid state. Not only the molecular and crystalline variety of sulfur contributes to this complexity but also the metastabihty of high-pressure phases which is related to the application of different experi-mentd procedures. For example, early structural studies on the p-T phase diagram of sulfur could not be performed in-situ. Therefore, in these experiments the sulfur samples were quenched from a selected temperature-pressure point to STP conditions. The results obtained by such a procedure depend strongly on the variables AT and Ap as well as on their time derivatives (gradients), dT/dt and dp/dt, respectively. Especially, dynamic compression (shock wave) methods may introduce further complications since melting of... 

Proton transfer dynamics of photoacids to the solvent have thus, being reversible in nature, been modelled using the Debye-von Smoluchowski equation for diffusion-assisted reaction dynamics in a large body of experimental work on HPTS [84—87] and naphthols [88-92], with additional studies on the temperature dependence [93-98], and the pressure dependence [99-101], as well as the effects of special media such as reverse micelles [102] or chiral environments [103]. Moreover, results modelled with the Debye-von Smoluchowski approach have also been reported for proton acceptors triggered by optical excitation (photobases) [104, 105], and for molecular compounds with both photoacid and photobase functionalities, such as lO-hydroxycamptothecin [106] and coumarin 4 [107]. It can be expected that proton diffusion also plays a role in hydroxyquinoline compounds [108-112]. Finally, proton diffusion has been suggested in the long time dynamics of green fluorescent protein [113], where the chromophore functions as a photoacid [23,114], with an initial proton release on a 3-20 ps time scale [115,116]. 

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