Water supercells

At the end of the reaction time there was no unreacted amine as shown by the following test A 10-ml. aliquot was filtered through Supercel to remove the manganese dioxide, and the filtrate was added to a mixture of 25 ml. of benzene and 25 ml. of water. Extraction of the benzene layer with 10% hydrochloric acid, followed by the addition of sodium hydroxide, gave no oil layer or characteristic odor of the free amine. 

A mixture of 6-aminocaproic acid (13 g, 0.1 mol) and phosphorous acid (12.7 g, 0.156 mol) in chlorobenzene (100 ml) was heated to 100°C with stirring. Phosphorus trichloride (22 g, 0.16 mol) was added drop-wise to the mixture within a period of 30 min. The solution was then heated with stirring for 3 h. Insoluble material separated during this time. After cooling, the solvent was decanted, and the residue was boiled with water (60 ml) for 30 min and subjected to hot filtration with activated charcoal through a layer of Supercel. The solution was concentrated under reduced pressure and the crystals formed were collected by filtration. Methanol was added to the mother liquors to complete the precipitation. There was in this way isolated pure 6-amino-l-hydroxyhexylidenediphosphonic acid (15 g, 55%) of mp 245°C. 

A mechanically stirred suspension of crude amino-sulfonamide hydrochloride salt (26.4 g, 73 mmol) in water (70 mL) was heated at 90°-95°C until all of the solid dissolved. To the hot solution was added activated carbon (Darco KB, 0.26 g), and the mixture stirred for 15 min at 90°-95°C. The mixture was filtered hot (85°-90°C) through a well-washed bed of filter aid (SuperCel). The filter cake was washed with boiling water (9 mL). The filtrate and cake wash were combined, and the product allowed to crystalize as well-stirred solution was cooled to 60°C. The mixture was stirred for 1 h at 60°C, or until the product had convened to the thermodynamically more stable hemihydrate crystal form. The mixture was then slowly cooled to 3°C, and then stirred for 1 h at this temperature. The mixture was filtered cold, using the mother liquors to rinse the cake. The product was air-dried, then dried in vacuo (100 mBar, nitrogen sweep, 45°-50°C) to constant weight. Yield 24.2 g (92% yield 59% overall yield from hydroxysulfone) of pure aminosulfonamide hydrochloride salt (dorsolamide) as a white crystalline solid. HPLC 99.9 area % (254 nm), 99.6 wt % vs an external standard, >99% (4S,6S) as the N-TFA derivative. Specific Rotation a589 =-17.1° (c=1.00, H20). MP 238°C. 

Upon determination of the completion of the reaction 20.0 g of 10 wt. % of aqueous sodium hydrogen sulfate solution was added in one portion, and the resultant admixture stirred for 10 min at ambient temperature. The batch was then concentrated in vacuo at 45°C to dryness. Subsequently water (180 g), toluene (69 g), ethyl acetate (36 g) were added and vigorous stirring for about 10 min undertaken. The resulting layers were separated and the aqueous layer saved in a flask. The organic layer was washed thrice with a solution of 26 ml of 2.5% HCI. The combined aqueous layers were then filtered through a pad of wet (with water) hyflo-supercel filter aid. Subsequently, EtOAc (85 g) was added to the filtrate and concentrated... 

Upon the reaction was complete, the batch was cooled to ambient temperature under the nitrogen atmosphere, and the contents filtered over a hyflo-supercel filtering pad (3.0 g, wetted with water). The flask and wet cake were rinsed with acetic acid (20 g). The filtrate was concentrated in vacuo to... 

Supercel, and the residue is washed with two 160-mI. portions of 95% ethanol. The combined filtrates are evaporated under reduced pressure with a rotary evaporator. The solid residue is heated in 400 ml. of boiling water and freed from a small amount of insoluble matter by decantation through a plug of glass wool placed in a filter funnel. The filtrate is chilled in an ice bath and ihe precipitate is collected by suction filtration, washed, and dried under vacuum. 

Adding a single water molecule per supercell, the barrier was reduced by somewhat more than 10 kcal/mol. The simulations showed clearly that the water molecule was active in the proton-transfer process that is needed to change the keto form to the enol form. Thus, the solvent does not only provide an external potential in which the molecule is moving, but takes active part in the transition. Having not only one water molecule per supercell but 28, the barrier was reduced by another 8 kcal/mol. In this case, the hydrogen transfer involves several water molecules and can be described as a Grotthuss like mechanism. 

Fig. 10. Pair correlation functions obtained both from Car-Parrinello simulations and from experiments. The thick solid lines are simulation results obtained using a supercell with 64 water molecules. The thin solid lines are for the 32-water molecule simulation. The short-dashed line is from experimental neutron scattering results (Soper et al., 1997), and the long-dashed line is from an X-ray study. Reprinted with permission from Silvestrelli and Parrinello (1999).

The kaolinite surfaces were hydrated at two different levels. Either 55 or 89 water molecules were added to the supercell pore and distributed on the surfaces during 15 ps of molecular dynamics simulations to create hydrated mineral surfaces. On a dry clay basis, these systems contained 24 and 39% water, respectively. Then, four TCE molecules were added to the center of each slit-pore and each system was equilibrated for at least 50 ps. In this and all other calculations a time step of 0.5 fs was used. 

Six unit cells of pyrophyllite were fused to produce an Al24Si48012o(OH)24 supercell of neutral, idealized 2 1 clay. Again, we expanded the interlayer space, in this case to 3.0 nm, and inserted 76 water molecules to give a water content of 32% by weight. We equilibrated the water for 15 ps at constant volume, and then inserted eight TCE molecules into the center of the interlayer space. This time, the molecular dynamics were run in the isothermal-isobaric (NPT) ensemble to simulate TCE in a fully hydrated micropore environment with no liquid-gas interfaces. 

The concentrate was saturated with potassium carbonate and stirred with three successive portions of chloroform (6, 3, and 2 1.). Concentration of the chloroform gave 200 g. of brown, basic, and neutral materials. This residue was dissolved in 4 1. of benzene and stirred, first with 2 1. and then with 11. of 5% tartaric acid. The combined aqueous solutions were stirred with 11. of water and then filtered through Hyfio Supercel to disperse a heavy emulsion. 

Figure 1. Geometrical arrangement of the slab model. The periodic supercell is replicated into three directions one side of the contains the metal slab, the other side the vacuum or water phase. The top view of the surface shows a typical arrangement for a V3xV3 unit cell, in this case representing an alloy AjB.

A model for a hydrated powder of MBP was constructed based on a crystal structure (PDB entry 1JW4 [20]). The model contained four protein molecules generated from four unit cells (a 2a x 2b x c lattice) of the triclinic crystal with the water molecules removed. A large box of water molecules was overlaid on the protein supercell, and all but the 3460 water molecules that were closest to the protein molecules were removed to give h = 0.43, corresponding to samples used in neutron scattering experiments carried out in conjunction with the simulations [8]. A constant pressure and temperature MD simulation at 1 atm and 300 K was used to allow the cell to collapse and anneal the protein-protein and protein-water contacts. A series of production runs were performed at constant pressure over a range of temperature. 

An alternative description of a molecular solvent in contact with a solute of arbitrary shape is provided by the 3D generalization of the RfSM theory (3D-RISM) which yields the 3D correlation functions of interaction sites of solvent molecules near the solute. It was first proposed in a general form by Chandler, McCoy, and Singer [22] and recently developed by several authors for various systems by Cortis, Rossky, and Friesner [23] for a one-component dipolar molecular liquid, by Beglov and Roux [24, 25] for water and a number of organic molecules in water, and by Hirata and co-workers for water [26, 27], metal-water [26, 28] and metal oxide-water [31] interfaces, orientationally dependent potentials of mean force between molecular ions in a polar molecular solvent [29], ion pairs in aqueous electrolyte [30], and hydration of hydrophobic and hydrophilic solutes alkanes [32], polar molecule of carbon monoxide [33], simple ions [34], protein [35], amino acids and polypeptides [36, 37]. It should be noted that accurate calculation of the solvation thermodynamics for ionic and polar solutes in a polar molecular liquid requires special corrections to the 3D-RISM equations to eliminate the electrostatic artifacts of the supercell treatment employed in the 3D-RISM approach [30, 34]. 

Figure 4.29 depicts the water site distribution profiles averaged along the metal slab surface, as a function of the -coordinate across the supercell. A layering of water molecules near the metal surface is clearly seen. The distance Az = z — from the first surface layer of metal atoms to the oxygen and hydrogen peaks of the first hydration layer practically coincide in position, = 2.47 A and = 2.52 A,... 

The 3D-RISM-MCSCF approach has been applied to carbon monoxide (CO) solute in ambient water [33]. Since it is known that the Hartree-Fock method predicts the electronic structure of CO in wrong character [167], the CASSCF method (2 core, 8 active orbitals, 10 electrons) in the basis sets of double zeta plus polarization (9s5pld/4s2pld) augmented with diffuse functions (s- and p-orbitals) was used. Water was described by the SPC/F model [127] and the site-centered local pseudopotential elaborated by Price and Halley for CP simulation [40]. The 3D-RISM/KH integral equations for the water distributions specified on a grid of 64 points in a cubic supercell of size 20 A were solved at each step of the SCF loop by using the method of modified direct inversion in the iterative subspace (MDIIS) [27, 29] (see Appendix). 

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