Molecular dynamic simulations hydrogen bonds

Keywords Ordered water monolayer, room temperatme, molecular dynamics simulations, hydrogen bonds, hydrophobicity/hydrophilicity, ethanol molecules... 

Example If a drug molecule interacts with a receptor molecule through hydrogen bonds, then yon might restrain the distance between the donor and acceptor atoms involved in the hydrogen bonds. During a molecular dynamics simulation, these atoms would slay near an ideal value, while the rest of the molecular system fully relaxes. 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

FIG. 26 Optimized structure of a water monolayer on mica obtained from molecular dynamic simulations by Odelius et al. The water molecules and the first layer of sihca tetrahedra of the mica substrate are shown in a side view in the top. K ions are the large dark balls. The bottom drawing shows a top view of the water. Oxygen atoms are dark, hydrogen atoms light. Notice the ordered icelike structure and the absence of free OH groups. All the H atoms in the water are involved in a hydrogen bond to another water molecule or to the mica substrate. (From Ref. 73.)... 

El Tayar, N., Mark, A. E., Vallat, P., Bmnne, R. A., Testa, B. and van Gunsteren, W. E. Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A evidence from partition coefficients and molecular dynamics simulations, J.Kled. Chem., 36 (1993), 3757-3764... 

J. M. Andanson, J. C. Soetens, T. Tassaing, andM. Besnard, Hydrogen bonding in supercritical tert butanol assessed by vibrational spectroscopies and molecular dynamics simulations. J. Chem. Phys. 122, 174512 (2005). 

Monte Carlo and Molecular Dynamics simulations of water near hydrophobic surfaces have yielded a wealth of information about the structure, thermodynamics and transport properties of interfacial water. In particular, they have demonstrated the presence of molecular layering and density oscillations which extend many Angstroms away from the surfaces. These oscillations have recently been verified experimentally. Ordered dipolar orientations and reduced dipole relaxation times are observed in most of the simulations, indicating that interfacial water is not a uniform dielectric continuum. Reduced dipole relaxation times near the surfaces indicate that interfacial water experiences hindered rotation. The majority of simulation results indicate that water near hydrophobic surfaces exhibits fewer hydrogen bonds than water near the midplane. 

Far IR spectroscopy is a useful technique to study the structural environment and dynamics of water molecules and ions in the interlayer galleries of LDHs, since it directly probes the intermolecular and hydrogen bonding interactions [223]. Spectra, which can be recorded by pressing small amounts of powder onto one side of a piece of Scotch tape, are often difficult to interpret because of the complex network of intermolecular interactions present and molecular dynamics simulations have been employed in order to assist in the interpretation [223]. 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

Fig. 4.1 a Typical time evolution of a given correlation function in a glass-forming system for different temperatures (T >T2>...>T ), b Molecular dynamics simulation results [105] for the time decay of different correlation functions in polyisoprene at 363 K normalized dynamic structure factor at the first static structure factor maximum solid thick line)y intermediate incoherent scattering function of the hydrogens solid thin line), dipole-dipole correlation function dashed line) and second order orientational correlation function of three different C-H bonds measurable by NMR dashed-dotted lines)... 

Figure 14. A stereoview of a typical "snapshot" from a molecular dynamics simulation of a-D-glucopyranose in aqueous solution, showing selected water molecules close to the 01 and 02 hydroxyl groups. The hydrophobic hydration requirements of the aliphatic hydrogen atoms on Cl and C2 impose additional structuring restrictions of the orientations of the water molecules hydrogen bonding to the 02 hydroxyl group. (Reproduced from Ref. 32. Copyright 1989 American Chemical Society.)...

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