Supporting Information

Dendrimer Building ToolKit: Model Building and Characterization of Various Dendrimer Architectures

Vishal Maingi,[a] Vaibhav Jain,[b] Prasad V. Bharatam*[c] and Prabal K. Maiti*[a]

[a]Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science,

Bangalore 560 012, India

[b]Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India

[c]Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India

*For correspondence: (P.K.M.) or (P.V.B.)

These are set of commands that were used in AMBER TOOLS 1.2 to have residue cap charge be zero, as well as same time whole residue to have integral charge (+/- 0,1,2....)

espgen -i your_esp.out -o your.esp

antechamber -i your_esp.out -fi gout -o your.ac -fo ac

respgen -i your.ac -o your.respin1 -f resp1 -a my_constraint.in

gedit (bash command) your.respin1

(for this remove all blank line/s BETWEEN last line and secondlast line and save it)

respgen -i your.ac -o your.respin2 -f resp2 -a my_constraint.in

gedit (bash command) your.respin2

(for this remove all blank line/s BETWEEN last line and secondlast line and save it)

resp -O -i your.respin1 -o your.respout1 -e your.esp -t your_q1

resp -O -i your.respin2 -o your.respout2 -e your.esp -q your_q1 -t your_q2

antechamber -i your.ac -fi ac -o your.mol2 -fo mol2 -c rc -cf your_q2

parmchk -i your.mol2 -f mol2 -o your.frcmod

Table S1. Various GAFF atom types along with the partial atomic charges has been depicted here for four residues used for building PAMAM dendrimer at neutral pH and high pH. Please note, to avoid confusion cap charges have not been included.

Central Core Residue ‘aaa' / Repeating Residue ‘bbb'
Atom / GAFF
atom type / Charge / Atom / GAFF atom type / Charge
C / c3 / 0.0289 / C / c3 / 0.4418
H / h1 / 0.0846 / H / h1 / -0.0353
H / h1 / 0.0846 / H / h1 / -0.0353
C / c3 / 0.0289 / C / c3 / -0.2825
H / h1 / 0.0846 / H / h1 / 0.1571
H / h1 / 0.0846 / H / h1 / 0.1571
N / n3 / -0.6577 / N / n3 / -0.7409
N / n3 / -0.6577 / C / c3 / 0.5168
C / c3 / 0.3694 / H / h1 / -0.0523
H / h1 / 0.0065 / H / h1 / -0.0523
H / h1 / 0.0065 / C / c3 / 0.5168
C / c3 / 0.3694 / H / h1 / -0.0523
H / h1 / 0.0065 / H / h1 / -0.0523
H / h1 / 0.0065 / C / c3 / -0.6039
C / c3 / 0.3694 / H / hc / 0.1673
H / h1 / 0.0065 / H / hc / 0.1673
H / h1 / 0.0065 / C / c3 / -0.6039
C / c3 / 0.3694 / H / hc / 0.1673
H / h1 / 0.0065 / H / hc / 0.1673
H / h1 / 0.0065 / C / c / 0.7211
C / c3 / -0.5435 / C / c / 0.7211
H / hc / 0.1589 / O / o / -0.6195
H / hc / 0.1589 / O / o / -0.6195
C / c3 / -0.5435 / N / n / -0.4658
H / hc / 0.1589 / H / hn / 0.3148
H / hc / 0.1589
C / c3 / -0.5435
H / hc / 0.1589
H / hc / 0.1589
C / c3 / -0.5435
H / hc / 0.1589
H / hc / 0.1589
C / c / 0.6780
C / c / 0.6780
C / c / 0.6780
C / c / 0.6780
O / o / -0.6049
O / o / -0.6049
O / o / -0.6049
O / o / -0.6049
Terminal Residue ‘ccc’ / Terminal Residue ‘ccc’ protonated
Atom / GAFF atom type / Charge / Atom / GAFF atom type / Charge
C / c3 / -0.0466 / N / n / -0.2641
H / h1 / 0.1090 / H / hn / 0.2763
H / h1 / 0.1090 / C / c3 / -0.1790
C / c3 / 0.5002 / C / c3 / 0.0800
H / h1 / -0.0303 / H / h1 / 0.1387
H / h1 / -0.0303 / H / h1 / 0.1387
N / n3 / -1.1895 / H / hx / 0.0779
H / hn / 0.4139 / H / hx / 0.0779
H / hn / 0.4139 / N / n4 / -0.1678
N / n / -0.5870 / H / hn / 0.2738
H / hn / 0.3376 / H / hn / 0.2738
H / hn / 0.2738

Table S1. contd.

Table S2. Various GAFF atom types along with the partial atomic charges has been depicted here for five residues used for building PPI dendrimer at neutral pH and high pH. Please note, to avoid confusion cap charges have not been included.

Central Core Residue ‘aaa' / Repeating Residue ‘bbb' / Terminal Residue ‘ccc'
Atom / GAFF atom type / Charge / Atom / GAFF atom type / Charge / Atom / GAFF atom type / Charge
N / n3 / -0.3927 / N / n3 / 0.4291 / C / c3 / 0.1814
C / c3 / -0.0106 / C / c3 / -0.0433 / H / h1 / 0.0409
C / c3 / 0.0947 / C / c3 / -0.0343 / H / h1 / 0.0409
C / c3 / 0.0947 / H / h1 / 0.0687 / N / n3 / -1.0377
C / c3 / -0.0106 / H / h1 / 0.0687 / H / hn / 0.3873
N / n3 / -0.3927 / C / c3 / -0.0433 / H / hn / 0.3873
C / c3 / -0.0300 / C / c3 / -0.0343
C / c3 / -0.0080 / H / hc / 0.0409
C / c3 / -0.0300 / H / hc / 0.0409
C / c3 / -0.0080 / C / c3 / 0.0738
C / c3 / -0.0300 / H / h1 / 0.0687
C / c3 / -0.0080 / H / h1 / 0.0687
C / c3 / -0.0300 / H / hc / 0.0409
C / c3 / -0.0080 / H / hc / 0.0409
H / h1 / 0.0453 / H / h1 / 0.0359
H / h1 / 0.0453 / H / h1 / 0.0359
H / hc / -0.0169
H / hc / -0.0169
H / hc / -0.0169
H / hc / -0.0169
H / h1 / 0.0453
H / h1 / 0.0453
H / h1 / 0.0575
H / h1 / 0.0575
H / hc / 0.0245
H / hc / 0.0245
H / h1 / 0.0575
H / h1 / 0.0575
H / hc / 0.0245
H / hc / 0.0245
H / h1 / 0.0575
H / h1 / 0.0575
H / hc / 0.0245
H / hc / 0.0245
H / h1 / 0.0575
H / h1 / 0.0575
H / hc / 0.0245
H / hc / 0.0245
Residue ‘bbb' protonated / Residue ‘ccc' protonated
Atom / GAFF atom type / Charge / Atom / GAFF atom type / Charge
N / n4 / 0.0606 / C / c3 / 0.2981
C / c3 / -0.0903 / H / hx / 0.0573
C / c3 / 0.0906 / H / hx / 0.0573
H / hx / 0.0932 / N / n4 / -0.4140
H / hx / 0.0932 / H / hn / 0.3337
C / c3 / -0.0903 / H / hn / 0.3337
C / c3 / 0.0906 / H / hn / 0.3337
H / hc / 0.0340
H / hc / 0.0340
C / c3 / 0.1590
H / hx / 0.0932
H / hx / 0.0932
H / hc / 0.0340
H / hc / 0.0340
H / hx / 0.0582
H / hx / 0.0582
H / hn / 0.2758

Table S3. Various GAFF atom types along with the partial atomic charges has been depicted here for four residues used for building PETIM dendrimer at neutral pH and high pH. Please note, to avoid confusion cap charges have not been included.

Central Core Residue ‘aaa' / Repeating Residue ‘bbb'
Atom / GAFF Atom Type / Charge / Atom / GAFF Atom Type / Charge
N / n3 / -0.6542 / N / n3 / -0.5969
C / c3 / 0.0518 / C / c3 / 0.1014
H / h1 / 0.0648 / H / h1 / 0.0441
H / h1 / 0.0648 / H / h1 / 0.0441
C / c3 / 0.0518 / C / c3 / 0.1014
H / h1 / 0.0648 / H / h1 / 0.0441
H / h1 / 0.0648 / H / h1 / 0.0441
C / c3 / 0.0518 / C / c3 / -0.0020
H / h1 / 0.0648 / H / h1 / 0.0506
H / h1 / 0.0648 / H / h1 / 0.0506
C / c3 / 0.0787 / C / c3 / -0.0161
H / hc / 0.0868 / H / hc / 0.0494
H / hc / 0.0868 / H / hc / 0.0494
C / c3 / 0.0787 / C / c3 / 0.1136
H / hc / 0.0868 / H / hc / 0.0627
H / hc / 0.0868 / H / hc / 0.0627
C / c3 / 0.0787 / C / c3 / 0.1136
H / hc / 0.0868 / H / hc / 0.0627
H / hc / 0.0868 / H / hc / 0.0627
C / c3 / -0.7494 / C / c3 / 0.0586
H / h1 / 0.2669 / H / h1 / 0.0612
H / h1 / 0.2669 / H / h1 / 0.0612
C / c3 / -0.7494 / C / c3 / -0.7242
H / h1 / 0.2669 / H / h1 / 0.2564
H / h1 / 0.2669 / H / h1 / 0.2564
C / c3 / -0.7494 / C / c3 / -0.7242
H / h1 / 0.2669 / H / h1 / 0.2564
H / h1 / 0.2669 / H / h1 / 0.2564
O / os / -0.2003

Table S3. contd.

Terminal Residue ‘ccc’ / Terminal Residue ‘ccc’ protonated
Atom / GAFF Atom Type / Charge / Atom / GAFF Atom Type / Charge
C / c3 / 0.6021 / C / c3 / 0.1706
H / h1 / -0.0925 / H / hx / 0.0421
H / h1 / -0.0925 / H / hx / 0.0421
C / c3 / -0.0254 / C / c3 / -0.0450
H / hc / 0.0085 / H / hc / 0.0265
H / hc / 0.0085 / H / hc / 0.0265
C / c3 / -0.0407 / C / c3 / 0.0473
H / h1 / 0.0461 / H / h1 / 0.0703
H / h1 / 0.0461 / H / h1 / 0.0703
N / n3 / -1.1180 / N / n4 / -0.2106
H / hn / 0.3842 / H / hn / 0.2840
H / hn / 0.3842 / H / hn / 0.2840
O / os / -0.1106 / O / os / -0.0920
H / hn / 0.2840

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