Molecular dynamics benzene

FIQ. 3 Diffusion coefficient of benzene molecules in benzene-polystyrene mixtures normalized by the diffusion coefficient of neat benzene molecular dynamics results, NMR measurements and prediction by the Mackie-Meares model [26]. 

As pointed out by Warshel and co-workers, the derivation of the important relation (14) is based on the assumption of non-saturation of the dielectric medium, which does not necessarily applies in the case of a macromolecule in solution [43]. These authors have shown that the validity of relation (14) could be directly tested by simulating the dipole motions through molecular dynamics models [43, 44, 45]. Detailed numerical calculations were carried out for the selfexchange reaction of cytochrome c [43], and for the electron transfer between two benzene-like molecules in water [45]. A similar approach was recently developed for the system (Fe " ", Fe ) in aqueous solution [46]. From these calculations, it was concluded that relation (14) applies provided that X is evaluated from a microscopic model. 

Sastre, G., Catlow, C.R.A., and Corma, A. (1999) Diffusion of benzene and propylene in MCM-22 zeolite a molecular dynamics study. J. Phys. 

Molecular dynamic simulations representing benzene in [MMIM]C1 and [MMIMJPFg established a correlation of the (high) solubility of benzene in ionic liquids with the strong electrostatic field around the aromatic molecule associated with the 7i-electrons. The high polarizability of benzene also contributes to the high solubility 94). 

Solvation dynamics of coumarin 153 in benzene-acetonitrile and benzene-methanol mixtures a Molecular Dynamics study... 

Molecular Dynamics study of the time-dependent fluorescence of coumarin 153 (C153 - see Fig. 1) in benzene-acetonitrile and benzene-methanol mixtures. The solvation dynamics in benzene-acetonitrile mixtures will be analyzed by inspection of the time-dependent local populations of the two constituents around the coumarin dye. 

In this work we presented the results of Molecular Dynamics simulations performed to study the solvatochromism and the dynamic stokes-shift of coumarin 153 in mixtures of solvents. We showed the ability of MD to reproduce available data of the time-dependent Stokes-shifts. Moreover, MD allowed us to interpret these dynamics in benzene-acetonitrile mixtures in terms of motions of benzene around the coumarin or rotation of acetonitrile. The role of benzene in the solvation process of Cl53 seems to be more important than usually assumed. 

Recent work by Zhang and LeBoeuf (in review) examined the effects of the presence of three solvents—water, acetone, and benzene—on the molecular mobility and structural relaxation of a humic acid through DSC analysis combined with molecular dynamics. Again, antiplasticization behavior was observed in two of the three systems (i.e., HA-water and HA-acetone) where solvents present in relatively low concentrations exhibited potential to form hydrogen bonds with the humic acid. Antiplasticization and plasticization behaviors were further interpreted from the perspective of hydrogen bonding analysis and free volume theory. 

In recent work (2008) ultrafast photolysis of a potential diazo ketone precursor of p-biphenylmethyloxirene failed to detect the oxirene, the UV absorption of which could, however, have been hidden by another band [8], and in a combined experimental/computational (ab initio and molecular dynamics with DFT) study, flash thermolysis of a formal Diels-Alder adduct was interpreted as affording acetylmethyloxirene and benzene [9]. 

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. 

Molecular-dynamic simulations are characterized by a solution of Newton s laws of motion for the molecules travelling through the zeolite pore system under control of the force field given by the properties of the host lattice, by interactions between the host and the molecules, and by interactions between the molecules. To date this has been possible only for the diffusion of simple molecules (e.g. methane or benzene) inside a zeolite lattice of limited dimensions [29, 37, 54], To take into account the effects of a chemical reaction as well would require quantum-mechanical considerations however, such simulations are in their infancy. 

At room temperature, these molecules occupy well-defined locations in their respective crystal lattices. However, they tumble freely and isotropically (equally in all directions) in place at their lattice positions. As a result, their solid phase NMR spectra show features highly reminiscent of liquids. We will see an illustration of this point shortly. Other molecules may reorient anisotropically (as in solid benzene). Polymer segmental motions in the melt may cause rapid reorientation about the chain axis but only relatively slow reorientation of the chain axes themselves. Large molecular aggregates in solution (such as surfactant micelles or protein complexes or nucleic acids) may appear to have solidlike spectra if their tumbling rates are sufficiently slow. There are numerous other instances in which our macroscopic motions of solid and liquid may be at odds with the molecular dynamics. Nuclear magnetic resonance is one of the foremost ways of investigating these situations. 

Figure 19 The definition of DP (left) and the results for several complexes based on CA M (right). Hub(M)3 and Flex(M)3 are discussed in the section on soluble aggregates Ad(M)3 I and Ad(M)3 II are similar to Hub(M)3, the primary difference is that adamantane instead of benzene is the central hub in the tripod [55]. The results from molecular dynamics (circles) and minimization calculations (squares) are shown...

Finally, dynamic structure-based pharmacophore models can be derived through a method first described by Carlson et al that uses multiple conformations of the target protein, which are obtained either by molecular dynamics simulation or by the use of multiple experimentally determined conformations. The binding sites of the respective snapshots are flooded with small molecular probes (e.g., methanol for hydrogen-bond interactions and benzene for aromatic hydrophobic interactions) and while the protein structure is held rigid the probe molecules are subjected to a low-temperature Monte Carlo minimization where they undergo multiple, simultaneous gas-phase... 

Monte Carlo and molecular dynamics calculations of the density profile of model system of benzene-water [70], 1,2-dichloroethane-water [71], and decane-water [72] interfaces show that the thickness of the transition region at the interface is molecu-larly sharp, typically within 0.5 nm, rather than diffuse (Fig. 4). A similar sharp density profile has been reported also at several liquid-vapor interfaces [73, 74]. The sharpness of interfaces thus seems to be a general characteristic of the boundary between two stable phases and it is likely that the presence of supporting electrolytes would not significantly alter the thickness of the transition region at an ITIES. The interfacial mixed solvent layer [54, 55], if any, would probably have a thickness comparable with this thin inner layer. 

FIGURE 14.2 Molecular dynamics simulation of the diffusion of benzene within a hydrated lipid bilayer membrane. Benzene molecules are shown as Corey-Pauling-Koltun (CPK) models atoms in the phospholipid head groups are shown as ball and stick models and hydrocarbon chains and water molecules as dark and light stick models, respectively. (Reproduced with permission from Bassolino-Klinaas D, Alper HE, Stouch TR. Biochemistry 1993 32 12624-37.)... 

A. Maliniak, A. Laaksonen, J. Kowalewski, and P. Stilbs, Molecular Dynamics Simulation Study of a Weakly Interacting System,Quinuclidine-Benzene, J. Chem. Phys., 89 (1988), 6434. 

M. Luhmer, A. Moschos, and J. Reisse, Intermolecular Dipole-dipole Spin Relaxation of Xenon-129 Dissolved in Benzene. A Molecular Dynamics Simulation Study, J. Magn. Reson., A113 (1995), 164-168. 

P. Linse, S. Engstrom, and B. Jonsson, Molecular Dynamics Simulation of Liquid and Solid Benzene, Chem. Phys. Lett., 115 (1985), 95-100. 

A. Vemov and W. A. Steele, Computer Simulations of Benzene Adsorbed on Graphite. 1. 85 K, Langmuir 7 (1991) 3110-3117 . 2. 298 K, ibid 2817-2820. References to experimental and other simulation studies of this system are contained in these papers. Also, A. Vemov and W. A. Steele Computer Simulations of Benzene Adsorbed on Graphite. 85 - 298 K, in Proc. 4 Int. Conf. On Fundamentals of Adsorption, ed. M. Suzuki, Kodansha Publishers, Tokyo, 1993, 695-701 M. A. Matties and R. Hentschke, Molecular Dynamics Simulation of Benzene on Graphite 1. Phase Behavior of an Adsorbed Monolayer, Langmuir 12 (1996) 2495-2500 2. Phase Behavior of Adsorbed Multilayers, ibid, 2501-2504. 

B. Clifton and T. Cosgrove, Simulation of Liquid Benzene between two Graphite Surfaces a Molecular dynamics Study, Mol. Phys. 93 (1998) 767-776. 

Molecular Dynamics (MD) and Monte Carlo (MC) studies of chlorobenzenes in a zeolite HY simulation box lead to results comparable to those with benzene in NaY. Insertion of halogen into the aromatic system does not change the dynamical behavior considerably. Also the replacement of the Na ions by protons seems to be of minor influence on such calculations. 

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