Water molecules diffraction

In general, anions are less strongly hydrated than cations, but recent neutron diffraction data have indicated that even around the halide ions there is a well defined primary hydration shell of water molecules, which, in... 

Molecular dynamics simulations of proteins often begin with a known structure (such as an X-ray diffraction structure) that you want to maintain during equilibration. Since the solvent may contain high energy hot spots, equilibration of the protein and solvent at the same time can change the protein conformation. To avoid this, select only the water molecules and run a molecular dynamics equilibration. This relaxes the water while fixing the protein structure. Then deselect the water and equilibrate the whole system. 

The stmcture of Pmssian Blue and its analogues consists of a three-dimensional polymeric network of Fe —CN—Fe linkages. Single-crystal x-ray and neutron diffraction studies of insoluble Pmssian Blue estabUsh that the stmcture is based on a rock salt-like face-centered cubic (fee) arrangement with Fe centers occupying one type of site and [Fe(CN)3] units randomly occupying three-quarters of the complementary sites (5). The cyanides bridge the two types of sites. The vacant [Fe(CN)3] sites are occupied by some of the water molecules. Other waters are zeoHtic, ie, interstitial, and occupy the centers of octants of the unit cell. The stmcture contains three different iron coordination environments, Fe C, Fe N, and Fe N4(H20), in a 3 1 3 ratio. 

These hydrated salts contain bidentate carbonate ligands and no water molecules are bound directly to the central metal atom. The only single-crystal x-ray diffraction studies available are those for salts of (4) (52—54) and the mineral tuliokite [128706 2-3], Na2BaTh(C03)2 -6H20], which contains the unusual Th(C02) 2 anion (5) (55). 

Protein crystals contain between 25 and 65 vol% water, which is essential for the crystallisation of these biopolymers. A typical value for the water content of protein crystals is 45% according to Matthews et al. l49,150). For this reason it is possible to study the arrangement of water molecules in the hydration-shell by protein-water and water-water interactions near the protein surface, if one can solve the structure of the crystal by X-ray or neutron diffraction to a sufficiently high resolution151 -153). 

Pandya et al. have used extended X-ray ascription fine structure (EXAFS) to study both cathodically deposited -Ni(OH)2 and chemically prepared / -Ni(OH)2 [44], Measurements were done at both 77 and 297 K. The results for / -Ni(OH)2 are in agreement with the neutron diffraction data [22]. In the case of -Ni(OH)2 they found a contraction in the first Ni-Ni bond distance in the basal plane. The value was 3.13A for / -Ni(OH)2 and 3.08A for a-Ni(OH)2. The fact that a similar significant contraction of 0.05A was seen at both 77 and 297K when using two reference compounds (NiO and / -Ni(OH)2) led them to conclude that the contraction was a real effect and not an artifact due to structural disorder. They speculate that the contraction may be due to hydrogen bonding of OH groups in the brucite planes with intercalated water molecules. These ex-situ results on a - Ni(OH)2 were compared with in-situ results in I mol L"1 KOH. In the ex-situ experiments the a - Ni(OH)2 was prepared electrochemi-cally, washed with water and dried in vac-... 

X-Ray diffraction analysis of oriented polysaccharide fibers has had a long history. Marchessault and Sarko discussed this topic in Volume 22 of Advances, and a series of articles by Sundararajan and Marchessault in Volumes 33, 35, 36, and 40 surveyed ongoing developments. The comprehensive account presented here by Chandrasekaran (West Lafayette, Indiana) deals with some 50 polysaccharides, constituting a wide range of structural types, where accurate data and reliable interpretations are available. The regular helical structures of the polysaccharide chains, and associated cations and ordered water molecules, are presented in each instance as stereo drawings and discussed in relation to observed functional properties of the polymers. 

Many ionic compounds contain what used to be referred to as water of crystallization . For example, magnesium chloride can exist as a fully hydrated salt which was formerly written MgCla.bHjO, but is more appropriately written Mg(OH2)eCl2, since the water molecules occupy coordination sites around the magnesium ions. This is typical. In most compounds that contain water of crystallization, the water molecules are bound to the cation in an aquo complex in the manner originally proposed by Alfred Werner (1866-1919) in 1893 (Kauffman, 1981). Such an arrangement has been confirmed in numerous cases by X-ray diffraction techniques. 

A number of other workers have reported the existence of an additional phase, corresponding to 4 1 5 (Feitknecht, 1930 Hayek, 1932 Aspelund, 1933), which may or may not be associated with a 1 1 1 phase. Feitknecht (1933) also carried out a detailed study of a phase described as 4 1 4 using X-ray diffraction and concluded that the material had a layer structure with interspersed water molecules. Such a structure would permit the addition and removal of water molecules without altering the interlayer... 

These special features are explained by an interaction between the proton and one of the water molecules, which is not merely electrostatic but also covalent. This yields a new chemical species, the hydroxonium ion, HjO. The existence of such ions was demonstrated in the gas phase by mass spectrometry and in the solid phase by X-ray diffraction and nuclear magnetic resonance. The H -H20 bond has an energy of 712kJ/mol, which is almost two-thirds of the total proton hydration energy. 

Interfacial water molecules play important roles in many physical, chemical and biological processes. A molecular-level understanding of the structural arrangement of water molecules at electrode/electrolyte solution interfaces is one of the most important issues in electrochemistry. The presence of oriented water molecules, induced by interactions between water dipoles and electrode and by the strong electric field within the double layer has been proposed [39-41]. It has also been proposed that water molecules are present at electrode surfaces in the form of clusters [42, 43]. Despite the numerous studies on the structure of water at metal electrode surfaces using various techniques such as surface enhanced Raman spectroscopy [44, 45], surface infrared spectroscopy [46, 47[, surface enhanced infrared spectroscopy [7, 8] and X-ray diffraction [48, 49[, the exact nature of the structure of water at an electrode/solution interface is still not fully understood. 

X-ray diffraction studies on several forms of the enzyme have demonstrated that the active site is composed of a pseudo-tetrahedral zinc center coordinated to three histidine imidazole groups and either a water molecule [(His)3Zn-OH2]2+ (His = histidine), or a hydroxide anion [(His)3Zn-OH] +, depending upon pH (156,157). On the basis of mechanistic studies, a number of details of the catalytic cycle for carbonic anhydrase have been elucidated, as summarized in Scheme 22... 

With data averaged in point group m, the first refinements were carried out to estimate the atomic coordinates and anisotropic thermal motion parameters IP s. We have started with the atomic coordinates and equivalent isotropic thermal parameters of Joswig et al. [14] determined by neutron diffraction at room temperature. The high order X-ray data (0.9 < s < 1.28A-1) were used in this case in order not to alter these parameters by the valence electron density contributing to low order structure factors. Hydrogen atoms of the water molecules were refined isotropically with all data and the distance O-H were kept fixed at 0.95 A until the end of the multipolar refinement. The inspection of the residual Fourier maps has revealed anharmonic thermal motion features around the Ca2+ cation. Therefore, the coefficients up to order 6 of the Gram-Charlier expansion [15] were refined for the calcium cation in the scolecite. 

Water intrusion-extrusion isotherms performed at room temperature on hydrophobic pure silica chabazite show that the water-Si-CHA system displays a real spring behavior. However, Pressure/Volume differences are observed between the first and the second cycle indicating that some water molecules interact with the inorganic framework after the first intrusion. 29Si and especially H solid state NMR and powder X-ray diffraction demonstrated the creation of new defect sites upon the intrusion-extrusion of water and the existence of two kinds of water molecules trapped in the super-cage of the Si-CHA a first layer of water strongly hydrogen bonded with the silanols of the framework and a subsequent layer of liquid-like physisorbed water molecules in interaction with the first water layer. 

---