S Reproduction o f the SPC/E model: prelim inary work

The amended ice slab described in section A.2.1 o f this chapter possessed the following statistics:

• Cell parameters: a = 22

Â,

A;

• Cell angles: a = p = 9 0 ° ,y = 120° • Cell density: 1.023gcm'^.

Simulations were initially performed on both hexagonal and cubic periodic systems o f 216 and 300 water m olecules (exclusively using Ih system later in the study), using a time step o f Ifs and a cut-off radius o f 9Â. Long range forces were treated using the Ewald summation technique. Microcanonical (NVE) dynamics were employed. The direct scaling method was used to maintain a constant temperature o f 273K. Each system was equilibrated for a period o f approximately 6ps followed by a production period o f 40ps simulation time, prior to analysing the trajectories.

T able A.2 below includes the results from Berensdsen et al}^ compared with the simulation results obtained from this work.

T able A .2. Preliminary results from SPC/E model.

SPC/E m odel [1 0 ] SPC/E model, (present work)

Density 0.998gcm'^ 1.023gcm'^

Pressure 6kPa 6.6Gpa

Potential Energy -41.7kJmor' -41.3kJmol''

The calculated values were obtained by performing constant N V T molecular dynamics on a bulk water system o f density approximately Igcm'^ at a temperature o f 300K for 60ps. The radial distribution functions calculated in this study from the water model are almost identical to the radial distribution functions calculated by Berensdsen et al., w hose own data was in good agreement with experimental data.

A. 3.1 Rationale

The justification for using an ice/water interface as opposed to an ice/vacuum interface is that the latter system is an unacceptable oversimplification. McDonald et al.}^ state that the ice/water interface describes the environment experienced by the ‘real’ m olecule in situ more accurately than the artificial environment used in simplified docking studies. However, adsorption studies utilizing an ice/vacuum system have proved insightful.^

A.4

Generation o f the ice-water interface : simulation method

A. 4.1 M ethodology

The generation o f the ice-crystal was explained previously in section A .2.1. The smooth, external (001) plane o f the ice slab w as modelled initially, a logical choice, since it occurs naturally in hexagonal ice.

A large block o f ice was made by duplicating a unit cell o f hexagonal ice. A custom made force field, containing the optimum parameter set was implemented [Table A . l ] in order to reproduce the SPC/E water model. The large block o f ice was orientated, displaying the [001] plane. The slab was rotated so that its smallest dimension was set to the z-direction. At this point, the slab contained four molecular layers o f width 3.6Â each in the z direction.

The co-ordinates in the slab o f ice containing 300 m olecules was duplicated in the ± z directions in order to provide the co-ordinates for what would becom e the liquid water region o f the structure. The ice/water interface was equilibrated in two stages o f N VE dynamics. The top and bottom portions o f the ice-slab were heated to 300K and equilibrated for lOps to produce a liquid phase. The positions o f all the atoms in the central (ice) portion were constrained during this stage. The system was then cooled to 273K and equilibrated for a further 6ps. The ice region was m odified to constrain all oxygen atoms whilst allowing the hydrogen atoms to m ove and the entire system was finally equilibrated for a further lOps at 273K. This resulted in an overall ice/water interface o f 2700 atoms in total. The resulting ice/water interface is shown in figure A.4.

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Figure A.4. The simulated ice/water interface.

A. 5

Sucrose

A. 5.1 Background

Although sucrose is a critical ingredient in commercially developed ice-creams, little is understood about its behaviour at a molecular level, both in a vacuum and at the ice/water interface. Sucrose is a disaccharide, composed from one D -glucose and one D-fructose unit, which are joined by an acetal linkage, an [ a P ( l - 2 ) glycosidic link] between two anomeric carbon atoms. The glucose unit is in the pyranose form and the fructose is in the furanose form. Since both the anomeric carbons are bound in the acetal form, sucrose is a non-reducing sugar, that is, no carbonyl groups are available to participate in chemical reactions.

The two torsional angles phi and psi were subtended at both o f the anomeric carbon centres o f the molecule. Figure A.5 shows a strained high energy conformation o f sucrose in which the functional groups are in extremely close proximity to each other leading to severe steric hindrance. Figure A.6 shows a less strained ‘anti’ conformation with less steric bulk. Figure A.7 shows the positions o f the phi/psi torsional angles whose flexibility lead to conformational changes.

O H