Molecular dynamics simulations, time-resolved

Q Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory... 

P. Suppan, Time-resolved luminescence spectra of dipolar excited molecules in liquid and solid mixtures - dynamics of dielectric enrichment and microscopic motions, Faraday Discuss., (1988) 173-84 L. R. Martins, A. Tamashiro, D. Laria and M. S. Skaf, Solvation dynamics of coumarin 153 in dimethylsulfoxide-water mixtures Molecular dynamics simulations, J. Chem. Phys., 118 (2003) 5955-63 B. M. Luther, J. R. Kimmel and N. E. Levinger, Dynamics of polar solvation in acetonitrile-benzene binary mixtures Role of dipolar and quadrupolar contributions to solvation, J. Chem. Phys., 116 (2002) 3370-77. 

We think that judicious application of molecular simulation tools for the calculation of thermophysical and mechanical properties is a viable strategy for obtaining some of the information required as input to mesoscale equations of state. Given a validated potential-energy surface, simulations can serve as a complement to experimental data by extending intervals in pressure and temperature for which information is available. Furthermore, in many cases, simulations provide the only realistic means to obtain key properties e.g., for explosives that decompose upon melting, measurement of liquid-state properties is extremely difficult, if not impossible, due to extremely fast reaction rates, which nevertheless correspond to time scales that must be resolved in mesoscale simulations of explosive shock initiation. By contrast, molecular dynamics simulations can provide converged values for those properties on time scales below the chemical reaction induction times. Finally,... 

Other Work on Water-Related Systems. Sonoda et al.61 have simulated a time-resolved optical Kerr effect experiment. In this model, which uses molecular dynamics to represent the behaviour of the extended medium, the principle intermolecular effects are generated by the dipole-induced-dipole (DID) mechanism, but the effect of the second order molecular response is also include through terms involving the static molecular / tensor, calculated by an MP2 method. Weber et al.6S have applied ab initio linear scaling response theory to water clusters. Skaf and Vechi69 have used MP2/6-311 ++ G(d,p) calculation of the a and y tensors of water and dimethylsulfoxide (DMSO) to carry out a molecular dynamics simulation of DMSO/Water mixtures. Frediani et al.70 have used a new development of the polarizable continuum model to study the polarizability of halides at the water/air interface. 

Figure 25. Molecular dynamics simulations of time-resolved Coulomb explosion of (Xe " clusters (N = 2-55 q = 1-10) (data from Ref. 93). The times for the doubling of the radius of the initial distribution of the Xe + ions scales as according to Eq. (114).

The photodissociation and recombination of I2 in solution have been studied for many decades as a prototype of a simple chemical reaction in solution. As mentioned earlier, transient X-ray diffraction signals for the photodissociation of I2 in hexane were calculated from molecular dynamics simulation back in 1986, in order to explore the potential of time-resolved X-ray scattering [8]. 

The principal aim of our study was to gain insights in the coupling mechanism between nuclear modes and electronic transition. To achieve this goal, we computed the time-resolved stimulated emission spectra in different regions of the p p transition. This involved carrying out molecular dynamic simulations of the hydrated bacterial reaction center of rb, sphaeroides in the ground and excited states of the special pair. 

Sagnella, D. E. Straub, J. E. Jackson, T. A. Lim, M. Anfinrud, P. A., Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carhonmonoxy myoglobin Comparison of time-resolved mid-lR absorbance experiments and molecular dynamics simulations. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 14324—14329. 

Molecular Dynamics Simulation of Time-Resolved Fluorescence and Nonequilibrium Solvation of Formaldehyde in Water. 

Keywords Block copolymer micelles Fluorescence anisotropy Fluorescence correlation spectroscopy Molecular dynamics simulations Monte Carlo simulations Solvent relaxation method Time-resolved fluorescence... 

Interpretation of Time-Resolved Fluorescence Anisotropy Data by Molecular Dynamics Simulations... 

This review of extensive molecular dynamics simulations of systems with relatively large numbers of atoms illustrates how it is now possible to begin the study of cooperative molecular motion involving interactions between skeletal vibrations and conformational isomers. Supercomputers have accomplished the extreme slow-motion display necessary to analyze simultaneous, cooperative changes. One can extrapolate that one more order of magnitude in atoms, and the extension of the analyzed time into the nanosecond range, can resolve many of the basic problems of the defect solid state of linear, flexible macromolecules. 

Kosovan P, Limpouchova Z, Prochazka K (2006) Molecular dynamics simulation of time-resolved fluorescence anisotropy decays liom labeled polyelectrolyte chains. Macromolecules 39(9) 3458-3465. doi 10.1021/ma052557a... 

---