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 () 59 735; E-mail: s.roy@ncl.res.in
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) -.86 3, 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
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) -.47 9, B, B amber99 9 ().7 amber99 8 (T) -.593 amber99 7 ().69 3, 6 CA, CB amber99 (CT) -.86 4, 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) -.5 9 amber99 7 ().8 3 CA amber99 (CT) -.8 3, 3 A, A amber99 9 ().5 33 CB amber99 (CT) -.3 34, 35, 36 B, B, B3 amber99 8 (C).7 3
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) -.47 9, 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) -.67 4, 5 A, A amber99 9 (). 6 CB amber99 (CT) -.34 7, 8, 9 B, B, B3 amber99 8 (C).6 4
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).339967.45773 amber99 7 ().698.656888 amber99 8 (C).64953.656888 amber99 9 ().4735.656888 amber99 38 ().35.78 amber99 8 (T).35.78 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 -. 3637. - CT.463 8.6 CT -.9 845. CT - CT.56 5948. CT - T.47 375.6 T -. 3637. CT - C.9 845. 5
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 - -. 9.88 - - CT 8.4 48.4 - CT - 9.5 48.4 - CT - CT. 669.4 CT - CT - 9.5 48.4 - CT - 9.5 9.8 CT - CT - T. 669.4 CT - T - 9.5 48.4 T - CT - 9.5 48.4 CT - T - CT 9.5 48.4 CT - CT - C 9.5 48.4 C - CT - C 9.5 9.8 - T - 9.5 9.88 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. 3.7656 3 - T - CT - CT. 3.7656 3 - T - CT -. 3.7656 3 CT - CT - T - CT..676 3 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.6584.9553. -.6338.. Table S8 Possible nearest neighbor (a, b) and next nearest neighbour (c, d and e) conformations for the PEI chain (c) (d) (e) 6
This journal is The Royal Society of Chemistry 5 6 Repeating Unit 6 7 4 4 7 5 n 8 3 5 3 8 9 3 4 9 6 -Terminal C-Terminal 4 3 6 7 5 8 9 4 Repeating Unit 7 8 3 3 6 9 n 5 4 5 n 9 33 8 3 6 7 3 3 34 35 36 -Terminal C-Terminal 4 3 (c) 6 7 Repeating Unit 3 8 9 4 5 8 4 7 n 6 9 5 3 5 6 7 9 8 -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
This journal is The Royal Society of Chemistry 4 36 -mer 5-mer p(r) Density (kg m -3 ) 3 8 4 7 7 7 73 74 75 76 77 78 79 8 Time (ns) Fig. S The variation of density of and 5-mer PEI with time. 8 6 End-to-end distance (nm) 8 7 6 5 4 3 5 5 3 35 4 45 5 Time (ns) 4 p(r)..5.3.35.4.45.5 Distance between, r (nm) 4 8 6 4.4.3.. 3 4 5 6 7 End-to-end distance (nm) Fig. S4 End-to-end distance and its distribution of -mer PEI for different protonation states..3.4.5.6.7.8 Distance between, r (nm) Fig. S3 The nearest neighbour, and The next nearest neighbour, distributions of the nitrogen atoms for the -mer PEI. 8
This journal is The Royal Society of Chemistry Radius of gyration (R g ) (nm).5.5.5.4.3.. unprototnated...3.4.5.6.7.8.9...3 Ratio (syn/trans).5 5 5 3 35 4 45 5 Time (ns).4.3.5.4...3. 4 6 8 4 6 8 Ratio (syn/trans)..6.8..4.6.8 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.5.4.3.. un [ -C-C- ] un [ C-C--C ] alternate [ -C-C- ] alternate [ C-C--C ] completely [ -C-C- ] completely [ C-C--C ]..5..5.3.35.4.45.5.55.6 Ratio (syn/trans).5.4.3. (d) - -5 - -5 5 5 Dihedral angle (Degrees) Fig. S6 Dihedral distribution for -mer PEI for different protonation states.. 3 4 5 6 7 8 9 3 4 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
This journal is The Royal Society of Chemistry g(r) 3.5.5.5 Residence time probability.4.35.3.5..5..5 st solvation st solvation protonated nd solvation nd solvation protonated..3.4.5.6.7.8.9.. r (nm) 5 5 5 3 35 4 45 5 Time (ps) g(r).5.5 Residence time probability.5.45.4.35.3.5..5. st solvation st solvation protonated nd solvation nd solvation protonated.5..3.4.5.6.7.8.9.. r (nm) 5 5 5 3 35 4 45 5 Time (ps) g(r).4..8.6.4. (c)..3.4.5.6.7.8.9.. 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.5.45.4.35.3.5..5..5 (c) st solvation st solvation protonated nd solvation nd solvation protonated 5 5 5 3 35 4 45 5 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.
This journal is The Royal Society of Chemistry MSD (nm ).5..5. 3 K 3 K 3 K 33 K 3 K 3 K 3 K 33 K.5 4 6 8 4 6 8 Time (ps) MSD (nm ).5.4.3. 3 K 3 K 3 K 33 K 3 K 3 K 3 K 33 K. 4 6 8 4 6 8 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.