Physical Chemistry Chemical Physics

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Supplementary Information

Dielectric Properties of Liquid Phase Molecular Clusters using External Field Method: Molecular Cite this: DOI: 10.1039/x0xx00000x Dynamics Study

Chathurika D. Abeyrathne,a,b Malka N. Halgamuge,b Peter M. Farrell,b and Efstratios Skafidasa,b Received 00th November 2013, Accepted 00thNovember 2013 aCentre for Neural Engineering (CfNE), bDepartment of Electrical and Electronic Engineering, The DOI: 10.1039/x0xx00000x University of Melbourne, Parkville, VIC 3010, Australia.

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Supplementary Information

Total Energy

3852 1300 Water 3850 Gly 1 M 1200 Ala 1 M 3848 Gaba 1 M

3846 1100

3844

1000 3842

3840 900

3838

Total Energy (kcal/mol)

Total Energy (kcal/mol) 800 3836

3834 700

3832 0 2 4 6 8 10 0 2 4 6 8 10 Electric Field [kcal/(molÅe)] Electric Field [kcal/(molÅe)]

Figure S1. Variation of total energy with electric field strength, (a) 1,4-dioxane, (b) water, Gly 1 M, Ala 1 M and GABA 1 M.

The accuracy of determining the slope of the dipole moment Radial Distribution Function variation curve is important for precise estimation of static dielectric constant. Thus, the energy of the system was studied as additional The structural changes of molecular clusters in the presence of information. The energy of the clusters was obtained from the output external electric fields can be obtained using the radial distribution of the MD simulation using VMD software. This gives the total function (RDF). The RDF was obtained from the trajectory file energy of the systems, that is, the sum of potential and kinetic generated from the MD simulations using VMD software. The energies. Figure S1 shows that the total energy of 1,4-dioxane and changes in RDFs of 1,4-dioxane and water are hardly outside the water is constant up to 10 kcal/(molÅe) (variation is less than 1 %), limits of statistical uncertainty for the field strengths concerned in and 1.5 kcal/(molÅe) (varies is less than 1%), respectively, whereas this study, indicating that there are no structural changes up to that of 1 M of bio-molecular aqueous solutions is constant up to 1.0 electric fields of 10 kcal/(molÅe) (4.334 × 107 V/cm). kcal/(molÅe) (varies is less than 1%). Thus, the slope of Fig. 1, 2 The structural changes of Gly 1 M are negligible, whereas and 3 was obtained by fitting up to linear equation where the small changes can be seen in Ala 1 M and considerable changes in variation of total energy is less than 1%. GABA 1 M are observed. The structural changes of Ala 1 M and GABA 1 M due to external electric fields are shown in Fig. S2 - S5. In these figures, nitrogen+–water, and nitrogen+-oxygen- RDFs of

This journal is © The Royal Society of Chemistry 2013 PCCP, 2013, 00, 1-3 | 1 ARTICLE Journal Name

Ala Gaba 1.6 1.6

1.4 -Water

-Water 1.4 +

N N 1.2 1.2

1 1

0.8 0.8 E = 0 E = 0 E = 2 E = 2 0.6 0.6 E = 4 E = 3 E = 6 E = 4 E = 8 0.4 0.4 E = 5 E = 10 E = 6

0.2 0.2

Radial Distribution Function, g Radial Distribution Function, g 0 0 0 2 4 6 8 10 0 2 4 6 8 10 Distance (Å) Distance (Å) + Figure S2. Radial distribution functions between N+ of alanine and Figure S4. Radial distribution functions between N of GABA and + water (N+-Water) for different electric fields. The unit of field water (N -Water) for different electric fields. The unit of field strength (E) is kcal/( molÅe). strength (E) is kcal/( molÅe).

Ala Gaba

90 30

- - E = 0

E = 0 -O

-O 80 E = 2 +

+ E = 2 N N E = 4 25 E = 3 70 E = 6 E = 4 E = 8 E = 5 E = 10 60 20 E = 6 E = 7 50 E = 8 15 E = 9 40 E = 10

30 10

20 5

10 Radial Distribution Function, g Radial Distribution Function, g

0 0 0 2 4 6 8 10 0 2 4 6 8 10

Distance (Å) Distance (Å)

+ - Figure S5. Radial distribution functions between N+ and O- of Figure S3. Radial distribution functions between N and O of + - alanine (N+-O-) for different electric fields. The unit of field strength GABA (N -O ) for different electric fields. The unit of field strength (E) is kcal/( molÅe). (E) is kcal/( molÅe).

alanine and GABA are presented. They can be considered to reflect the structural changes of pure water, alanine and GABA caused by external electric fields of various strengths. The electric fields affect the structure of alanine and water, as shown in Fig. S2 - S3. The RDF of nitrogen+- water of alanine shows a small change in the height of first minima indicating the broadening of first peak, though the positions of the first peaks are not affected by the application of an external field. Thus the density of water shows small changes in the presence of alanine due to external electric fields. Figure S3 illustrates that the height of first peak of nitrogen+-oxygen- RDF decreases where a considerable difference (12 %) can be seen at 10 kcal/(molÅe) (4.334 × 107 V/cm).

Figure S6. Orientation of GABA molecules when there is no external electric field.

Figure S7. Orientation of GABA molecules when the external electric field is 6 kcal/(molÅe).

Figure S8. Orientation of GABA molecules when the external electric field is 10 kcal/(molÅe).

The density of water molecules changes in the presence of GABA more than in the presence of alanine (Fig. S4). There is a large change in the RDF of nitrogen+-oxygen- of GABA after 5 kcal/(molÅe) (2.167 × 107 V/cm) as shown in Fig. S5. The height of first peak decreases and shifts with increasing field strength. The rotation of the GABA molecules caused by the external electrical field is shown in Fig. S6 - S8.