Water oxygen atoms

Figure 6 Radial distributions of water oxygen atoms around sites in the polar groups in a DPPC bilayer.

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.)... 

Fig. 5. Probabilities pn of observing n water-oxygen atoms in spherical cavity volumes v. Results from Monte Carlo simulations of SPC water are shown as symbols. The parabolas are predictions using the flat default model in Eq. (11). The center-to-center exclusion distance d (in nanometers) is noted next to the curves. The solute exclusion volume is defined by the distance d of closest approach of water-oxygen atoms to the center of the sphere. (Hummer et al., 1998a)... 

We assume for simplicity that the solvent is pure water, and that only the water-oxygen atoms have explicit Lennard-Jones interactions with the solute (this is typical of several common water models). We have seen that AWnp can be viewed as the free energy to change A from zero to one. Therefore, a well-known thermodynamic integration formula gives... 

In this compound, each Nd(III) ion is coordinated by six carboxylate and two water oxygen atoms. The Nd—0 distances are in the range of 2.3—2.6 A. The coordination polyhedron around Nd(III) has been described as a square antiprism. 

Figure 7. Water oxygen-exocyclic methylene carbon pair distribution function, calculated from a molecular dynamics simulation of a-D-glucopyranose in aqueous solution, giving the normalized probability of finding a water oxygen atom a given distance r from the C6 carbon atom. (Reproduced from Ref. 32. Copyright 1989 American Chemical Society.)...

The buried water molecule noticed in the crystal structure of this and many other inhibitor complexes is tetrahedrally coordinated to both the inhibitor and the flaps of the enzyme. Randad et al. (1993) have used molecular modelling based on the crystal structures to incorporate the water oxygen atom as the carbonyl oxygen of novel, cyclic ureas (67). They reasoned that displacement of the water should be energetically favourable... 

An interesting structural feature arises in the coordination of Li+ by urea in the complex Lil-2urea 62 each urea bridges two cations. This may be compared with LiCl-dioxane63 in which a related bridging occurs, and contrasted with NaCl-urea-H O64 in which the octahedral metal environment is due to two Cl- anions, two water oxygen atoms and two urea oxygen atoms. 

Figure 2. Experimental and simulated fluorescence Stokes shift function 5(f) for coumarin 343 in water. The curve marked Aq is a classical molecular dynamics simulation result using a charge distribution difference, calculated by semiempirical quantum chemical methods, between ground and excited states. Also shown is a simulation for a neutral atomic solute with the Lennard-Jones parameters of the water oxygen atom (S°). (From Ref. 4.)...

This is, of course, an aspect of the question that Pauling addressed and that led to the definition of the electroneutrality principle. If we consider the interaction of six water molecules with a Cr3+ ion, we may write two limiting valence bond structures. One of these forms localises the positive charge on the metal centre and depicts a Cr3+ ion surrounded by six water molecules. The covalent representation places a single positive charge on each of the water oxygen atoms and a —3 charge on the chromium centre (Fig. 2-13). 

In a neutron diffraction study of the ethylene oxide clathrate deuterohy-drate 6(CH2)20-46D20, the hydrogen-bonded host framework is defined by three independent deuterated water oxygen atoms occupying special positions, as shown in the table below. The deuterium atoms are located precisely as... 

With these definitions we get a correction for the one-center energy of the water oxygen atom due to partial electron density transfer to the acceptor orbital ... 

We also illustrate this for water protonation. The zeolite proton will attach to the water oxygen atom, The proton of water will bind to the basic lattice oxygen anion ... 

Fig. 12.3. Distribution of water molecules around trehalose. Cloud-like regions represent iso-probability surface of water oxygen atoms...

A second form of Nd2(malonate)3 6H2O complex has been reported [169]. In this complex neodymium is nine-coordinate surrounded by six carboxylate, and three water oxygen atoms and the geometry is intermediate between the distorted capped square antiprism and the distorted tricapped trigonal prism. 

The first serious attempt at interpreting the protein hydration by crystallographic methods was nude 1978 on rubvedoxin, a molecule consisting of only 54 amino adds [835]. The refinement by conventional (unconstrained) least squares methods included a total of 127 water sites and converged at an R-factor of 12.7% with 1.2 A resolution data. The water oxygen atoms were added to the model only if their temperature factors were <50 A2 and their electron density was >0.3 e/A3, i.e., corresponding to the electron density expected for liquid water, 0.34 e/A3. 

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