Molecular dynamics simulation comparison with experiment

The picosecond internal dynamics of myoglobin was explored by measuring inelastic neutron scattering by Smith et al. [25]. At low temperatures they found the dynamics to be harmonic while at higher temperatures a considerable quasielastic scattering was detected. Agreement between the experimentally observed spectra and that calculated from molecular dynamics simulations also showed evidence for restriction of the conformational space sampled at 80 K relative to 300 K. On the basis of these results it was concluded that the protein is trapped in local minima at low temperatures in accord with the multiple substate model suggested by low temperature flash photolysis experiments and previous molecular dynamics simulations. Comparison of atomic fluctuation data sets collected at both 325 K and 80 K confirms that the room temperature... 

Fig. 7 gives an example of such a comparison between a number of different polymer simulations and an experiment. The data contain a variety of Monte Carlo simulations employing different models, molecular dynamics simulations, as well as experimental results for polyethylene. Within the error bars this universal analysis of the diffusion constant is independent of the chemical species, be they simple computer models or real chemical materials. Thus, on this level, the simplified models are the most suitable models for investigating polymer materials. (For polymers with side branches or more complicated monomers, the situation is not that clear cut.) It also shows that the so-called entanglement length or entanglement molecular mass Mg is the universal scaling variable which allows one to compare different polymeric melts in order to interpret their viscoelastic behavior. 

A proposal for the comprehensive study of chemical processes in a variety of important condensed-phase systems using modern theoretical methodology has been presented. The primary goals of the research are to provide microscopic information on the mechanisms and structural and dynamical properties of the chemical systems proposed for investigation, to test the applicability of modern ab initio molecular dynamics (MD) by comparison with experiment, and to develop and apply novel ab initio MD techniques in simulating complex chemical systems. The proposed research will contribute to the forefront of modern theoretical chemistry and address a number of important technological issues. The PI has carefully attempted to demonstrate his knowledge, ability, and resources to carry out the proposed research projects. 

In the applications of the PCM approach to SD, the focus so far has been mainly on the comparison with experiment [45,46] and very good agreement with experimental results has been obtained for C153 in several polar liquids [45], In the case of SD in water, the theory was implemented using two different approaches to obtain e(w), either a fit to experimental data [45] or a calculation of the dipole density time correlation from molecular dynamics simulation [46], While the results for S(t) that use experimental dielectric permittivity as input look quite similar to those shown in Figure 3.16, the results based on the simulation data exhibit more pronounced oscillatory features at the characteristic frequency of the hydrogen bond librations. 

Since Poisson-Boltzmann theory neglects all ion-ion correlations (see Sect. 2.2) one is tempted to assume that their incorporation into the theoretical treatment would resolve the discrepancy. However, the comparison displayed in Fig. 8 shows clearly that these correlational effects can only be made responsible for a part of the deviations. Since the two different approaches, using a correlation-corrected density functional theory and Molecular Dynamics simulations, agree very well with each other, it becomes obvious that the discrepancy between them and the experiment is not due to the neglect of ionic correlations. 

The atomic radii may be further refined to improve the agreement between experimental and theoretical solvation free energies. Work on this direction has been done by Luque and Orozco (see [66] and references cited therein) while Barone et al. [67] defined a set of rules to estimate atomic radii. Further discussion on this point can be found in the review by Tomasi and co-workers [15], It must be noted that the parameterization of atomic radii on the basis of a good experiment-theory agreement of solvation energies is problematic because of the difficulty to separate electrostatic and non-electrostatic terms. The comparison of continuum calculations with statistical simulations provides another way to check the validity of cavity definition. A comparison between continuum and classical Monte Carlo simulations was reported by Costa-Cabral et al. [68] in the early 1980s and more recently, molecular dynamics simulations using combined quantum mechanics and molecular mechanics (QM/MM) force-fields have been carried out to analyze the case of water molecule in liquid water [69],... 

The solvated electron is a transient chemical species which exists in many solvents. The domain of existence of the solvated electron starts with the solvation time of the precursor and ends with the time required to complete reactions with other molecules or ions present in the medium. Due to the importance of water in physics, chemistry and biochemistry, the solvated electron in water has attracted much interest in order to determine its structure and excited states. The solvated electrons in other solvents are less quantitatively known, and much remains to be done, particularly with the theory. Likewise, although ultrafast dynamics of the excess electron in liquid water and in a few alcohols have been extensively studied over the past two decades, many questions concerning the mechanisms of localization, thermalization, and solvation of the electron still remain. Indeed, most interpretations of those dynamics correspond to phenomenological and macroscopic approaches leading to many kinetic schemes but providing little insight into microscopic and structural aspects of the electron dynamics. Such information can only be obtained by comparisons between experiments and theoretical models. For that, developments of quantum and molecular dynamics simulations are necessary to get a more detailed picture of the electron solvation process and to unravel the structure of the solvated electron in many solvents. 

Initiated by the chemical dynamics simulations of Bunker [37,38] for the unimolecular decomposition of model triatomic molecules, computational chemistry has had an enormous impact on the development of unimolecular rate theory. Some of the calculations have been exploratory, in that potential energy functions have been used which do not represent a specific molecule or molecules, but instead describe general properties of a broad class of molecules. Such calculations have provided fundamental information concerning the unimolecular dissociation dynamics of molecules. The goal of other chemical dynamics simulations has been to accurately describe the unimolecular decomposition of specific molecules and make direct comparisons with experiment. The microscopic chemical dynamics obtained from these simulations is the detailed information required to formulate an accurate theory of unimolecular reaction rates. The role of computational chemistry in unimolecular kinetics was aptly described by Bunker [37] when he wrote The usual approach to chemical kinetic theory has been to base one s decisions on the relevance of various features of molecular motion upon the outcome of laboratory experiments. There is, however, no reason (other than the arduous calculations involved) why the bridge between experimental and theoretical reality might not equally well start on the opposite side of the gap. In this paper... results are reported of the simulation of the motion of large numbers of triatomic molecules by... 

Whereas Eq.(5.58) serves for the determination of local interactions between cluster models of a zeolite and interacting molecules, analytical expressions are needed for the interaction potential if one wishes to compute vibrational frequencies for purpose of comparison with experiment or if the potentials are to be used in Monte Carlo or molecular-dynamics simulation calculations. Sauer and co-workers developed such analytical potentials for the water-silica interaction system. The method makes use of the molecular electrostatic potential (MEP) maps and the functional form of EPEN/2 (Empirical Potential based on interactions of Electrons and Nuclei). EPEN/2 potential functions consist of a point-charge interaction term and... 

Kairn, T., Daivis, P. J., Ivanov, I., and Bhattacharya, S. N., Molecular-dynamics simulation of model polymer nanocomposite rheology and comparison with experiment, J. Chem. Phys., 123, 194905-1 (2005). 

Frequently, molecular dynamics simulations are performed at conditions of constant pressure or temperature. In constant volume simulations, the volume of the simulation box is thought to be constant, although the pressure is changing. Simulations under these conditions represent only a rough estimate and the results must be verified by comparison with corresponding experiments. It turns out that in the simulation the values of T and P often have a crucial influence on the course of the computer simulation. 

Abstract We present in this contribution results from Molecular Dynamics (MD) simulations of a chemically realistic model of 1,4-polybutadiene (PB). The work we will discuss exemplifies the physical questions one can address with these types of simulations. We will specifically compare the results of the computer simulations with nuclear magnetic resonance (NMR) experiments, neutron scattering experiments and dielectric data. These comparisons will show how important it is to understand the torsional dynamics of polymers in the melt to be able to explain the experimental findings. We will then introduce a freely rotating chadn (FRC) model where all torsion potentials have been switched off and show the influence of this procedure on the qualitative properties of local dynamics through comparison with the chemically realistic (CRC) model. 

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