Structural and dynamical properties of Polyethylenimine in explicit water at different protonation states: A Molecular Dynamics Study

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1 This journal is The Royal Society of Chemistry Structural and dynamical properties of Polyethylenimine in explicit water at different protonation states: A Molecular Dynamics Study Chandan Kumar Choudhury a and Sudip Roy a Received Xth XXXXXXXXXX XX, Accepted Xth XXXXXXXXX XX First published on the web Xth XXXXXXXXXX X DOI:.39/bx a Physical Chemistry Division, ational Chemical Laboratory, Pune, India. Fax: +9 () 5965; Tel: +9 () ; s.roy@ncl.res.in

2 This journal is The Royal Society of Chemistry Table S Coulombic parameters (q i, see Equation ) for PEI chain. See Figure S for atom numbers. Atom o. Atom name Atom type Charge, q i amber99 38 () -.74, 3, amber99 7 ().5 4 CA amber99 (CT) -.4 5, 6, 8, 9 A, A, B, B amber99 9 ().5 7 CB amber99 (CT) -.8 amber99 8 (T) -.593, amber99 7 ().69, 5 CA, CB amber99 (CT) , 4, 6, 7 A, A, B, B amber99 9 ().4 8 amber99 8 (T) -.5 9, amber99 7 ().8 CA amber99 (CT) -.8, A, A amber99 9 ().5 3 CB amber99 (CT) -.3 4, 5, 6 B, B, B3 amber99 8 (C).7

3 This journal is The Royal Society of Chemistry Table S Coulombic parameters (q i, see Equation ) for alternate protonated PEI chain. See Figure S for atom numbers. Atom o. Atom name Atom type Charge, q i amber99 8 (T) -.47, 3, 4,, 3 amber99 7 ().36 5 CA amber99 (CT).56 6, 7 A, A amber99 9 ().87 8 CB amber99 (CT) , B, B amber99 9 ().7 amber99 8 (T) amber99 7 ().69 3, 6 CA, CB amber99 (CT) , 5, 7, 8 A, A, B, B amber99 9 ().4 9 amber99 8 (T) -.5,, amber99 7 ().34, 5 CA, CB amber99 (CT) -.3 3, 4, 6, 7 A, A, B, B amber99 9 ().9 8 amber99 8 (T) amber99 7 ().8 3 CA amber99 (CT) -.8 3, 3 A, A amber99 9 ().5 33 CB amber99 (CT) , 35, 36 B, B, B3 amber99 8 (C).7 3

4 This journal is The Royal Society of Chemistry Table S3 Coulombic parameters (q i, see Equation ) for completely protonated PEI chain. See Figure S(c) for atom numbers. Atom o. Atom name Atom type Charge, q i amber99 8 (T) -.47, 3, 4,, 3 amber99 7 ().36 5 CA amber99 (CT).56 6, 7 A, A amber99 9 ().87 8 CB amber99 (CT) , B, B amber99 9 ().7 amber99 8 (T) -.5, 3, amber99 7 ().34 4, 7 CA, CB amber99 (CT) -.3 5, 6, 8, 9 A, A, B, B amber99 9 ().9 amber99 8 (T) -.35,, amber99 7 ().33 3 CA amber99 (CT) , 5 A, A amber99 9 (). 6 CB amber99 (CT) , 8, 9 B, B, B3 amber99 8 (C).6 4

5 This journal is The Royal Society of Chemistry Table S4 Lennard Jones parameters (σ and ε, see Equation ) for the atom types mentioned in Table S, Table S, and Table S3. Atom type σ, nm ε, kj mol amber99 (CT) amber99 7 () amber99 8 (C) amber99 9 () amber99 38 () amber99 8 (T) Table S5 Bond parameters (b and ki bonds j, see Equation ) for the bond between the atom types (i j) in Table S, Table S and Table S3. Bond (Atom types, i j) b, nm ki bonds j, kj mol nm CT CT CT - CT CT - T T CT - C

6 This journal is The Royal Society of Chemistry Table S6 Bonded angle parameters (θ and k angle i jk ) for angles formed by the atom types (i jk) mentioned in Table S, Table S and Table S3. Angles (Atom types, i jk) θ, k angle i jk, kj mol rad CT CT CT - CT CT - CT CT CT - CT - T CT - T T - CT CT - T - CT CT - CT - C C - CT - C T Table S7 Dihedral parameters (φ s and ki dihedral jkl, see Equation ) for armonic functions and the values of C n for Ryckaert-Bellemans functions. X denotes any undefined atom types in the harmonic functions in Table S, Table S and Table S3 Dihedral (Atom types), i jkl φ s ki dihedral jkl (kj mol ) n - - CT - CT T - CT - CT T - CT CT - CT - T - CT CT - CT - T - CT 8..4 Dihedral (Atom types), i jkl, kj mol C C C C 3 C 4 C 5 X - - CT - X X - CT - CT - X Table S8 Possible nearest neighbor (a, b) and next nearest neighbour (c, d and e) conformations for the PEI chain (c) (d) (e) 6

7 This journal is The Royal Society of Chemistry 5 6 Repeating Unit n Terminal C-Terminal Repeating Unit n n Terminal C-Terminal 4 3 (c) 6 7 Repeating Unit n Terminal C-Terminal Fig. S Structure of PEI with atom number. Unprotonated chain, Alternate protonated, and (c) chain. For and chain n = 8 for -mer and 48 for 5-mer, while for alternated protonated chain, n = 9 and 4 for and 5-mer, respectively. The atoms are numbered for Table S,Table S and Table S3. 7

8 This journal is The Royal Society of Chemistry mer 5-mer p(r) Density (kg m -3 ) Time (ns) Fig. S The variation of density of and 5-mer PEI with time. 8 6 End-to-end distance (nm) Time (ns) 4 p(r) Distance between, r (nm) End-to-end distance (nm) Fig. S4 End-to-end distance and its distribution of -mer PEI for different protonation states Distance between, r (nm) Fig. S3 The nearest neighbour, and The next nearest neighbour, distributions of the nitrogen atoms for the -mer PEI. 8

9 This journal is The Royal Society of Chemistry Radius of gyration (R g ) (nm) unprototnated Ratio (syn/trans) Time (ns) Ratio (syn/trans) Radius of gyration (R g ) (nm).5.4 (c) Fig. S5 Radius of Gyration and its distribution of -mer PEI for different protonation states..3.. Probability un [ -C-C- ] un [ C-C--C ] alternate [ -C-C- ] alternate [ C-C--C ] completely [ -C-C- ] completely [ C-C--C ] Ratio (syn/trans) (d) Dihedral angle (Degrees) Fig. S6 Dihedral distribution for -mer PEI for different protonation states alternate syn-anti pairs Fig. S7 Distribution of ratio (syn/anti) when all, -C-C- and (c) C-C--C dihedrals were considered. (d) Alternate syn-anti occurrences of all the dihedrals for -mer PEI. 9

10 This journal is The Royal Society of Chemistry g(r) Residence time probability st solvation st solvation protonated nd solvation nd solvation protonated r (nm) Time (ps) g(r).5.5 Residence time probability st solvation st solvation protonated nd solvation nd solvation protonated r (nm) Time (ps) g(r) (c) r (nm) Fig. S8 The pair distribution plot of of PEI and O of Water, C of PEI and O of Water and (c) and C of PEI and O of Water for -mer PEI. Residence time probability (c) st solvation st solvation protonated nd solvation nd solvation protonated Time (ps) Fig. S9 Residence time probability of the water molecules in different solvation shells of the polymer chain (5-mer) at 3 K 3 K and (c) 33 K.

11 This journal is The Royal Society of Chemistry MSD (nm ) K 3 K 3 K 33 K 3 K 3 K 3 K 33 K Time (ps) MSD (nm ) K 3 K 3 K 33 K 3 K 3 K 3 K 33 K Time (ps) Fig. S Mean square displacement of water molecules around the st solvation shell, and nd solvation shell at different temperatures for (solid lines) and protonated (dotted - dashed lines) states of 5-mer PEI.