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Data are divided into the fitting set and test set as used in the parametrization of the GolP-CHARMM force field in J. Chem. Theory Comput. 2013, 9, 1616.

Supporting Information for Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Forcefield and Parametrization of Au-S Bonds Zdenek Futera and Jochen Blumberger1,2 1

University College London, Department of Physics and Astronomy and Thomas-Young-Centre, Gower Street, London WC1E 6BT, UK 2

Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 2 a, D-85748 Garching, Germany

S1

Table S1: Number of adsorbed structures N and adsorption energies [kJ/mol] obtained by experimental measurements or DFT calculations E (ref) and by GolP-CHARMM force field for which the lowest-obtained energy E (min), average energy E (avr) and standard deviation s (avr) of average energy are shown. Data are divided into the fitting set and test set as used in the parametrization of the GolP-CHARMM force field in J. Chem. Theory Comput. 2013, 9, 1616. Fitting set: Molecule Methane Ethane Butane Hexane Heptane Octane Nonane Ethene 1,3-butadiene Benzene Methanethiol Diethylsulfide Methylamine Imidazole Water

Label CH4 ETH BUT HEX HEP OCT NON ETE BDE BEN MTH DES MAM IMI WTR

N 44 44 47 49 48 48 50 47 50 46 45 47 47 50 49

E (ref) -14.5a / -14.2h -24.1a / -22.0h -40.5a / -39.2h -55.9a / -56.4h -62.7a / -64.6h -69.7a / -73.0h -75.2a / -81.5h -27.0a / -25.8h -46.2a / -45.4h -57.9a / -61.5b / -51.2h -48.0c / -58.0d / -42.1h -68.0a / -71.6h -54.8g / -53.9h -54.1g / -53.8h -18.3g / -17.6h

E (min) -13.3 -21.2 -37.0 -53.2 -60.9 -68.6 -75.6 -25.9 -41.9 -62.5 -51.8 -71.6 -33.1 -58.6 -11.2

E (avr) -12.6 -20.5 -34.3 -48.3 -55.3 -60.4 -66.8 -24.3 -40.8 -61.3 -51.0 -70.0 -32.2 -56.6 -10.1

s (avr) 0.3 0.4 3.2 4.7 5.1 5.6 6.5 0.6 0.5 0.4 0.6 1.1 0.5 0.5 0.6

Label CHX TBU NEN CHE TOL MOH ACT FMA AMM FMN ESH DBS

N 47 45 45 48 45 49 48 49 50 42 47 48

E (ref) -50.6 / -50.0f / -45.5h -41.7a / -43.5h -76.2a / -84.9h -54.0f / -54.3h -66.1a / -61.2h -30.5g / -29.2h -41.0e / -38.0h -29.2g / -26.9h -38.1h -34.2g / -35.6h -51.0a / -49.4h -86.0a / -103.3h

E (min) -43.5 -39.2 -75.5 -47.3 -69.6 -26.5 -43.6 -27.2 -27.1 -35.4 -55.4 -95.5

E (avr) -42.3 -38.4 -62.7 -46.5 -68.3 -25.3 -42.4 -26.1 -25.6 -34.4 -54.6 -88.4

s (avr) 0.5 0.4 15.6 0.4 0.4 0.5 0.5 0.5 0.6 0.5 0.5 3.8

Test set: Molecule Cyclohexane trans-2-butene Non-1-en Cyclohexene Toluene Methanol Acetone Formic acid Ammonia Formamide Ethanethiol Dibutylsulfide

a

a

Exp. data from J. Phys. Chem. B 1998, 102, 9266; bExp. data from J. Phys. Chem. B 2001, 105, 8387; cExp. data from J. Phys. Chem. B 1998, 102, 3456; dExp. data from J. Am. Chem. Soc. 1987, 109, 733; eExp. data from Surf. Sci. 2002, 498, 53; fExp. data from Surf. Sci. 2002, 498, 61; gplanewave revPBE-vdW data from J. Chem. Theory Comput. 2013, 9, 1616; hrevPBE-vdW data from this work.

S2

Table S2: Number of adsorbed structures N and adsorption distances [Å] obtained by revPBEvdW d (ref) and GolP-CHARMM force field for which adsorption distance of the lowest-energy structure d (min), average adsorption distance d (avr) and average distance between surface plane and molecular center of mass d (com) are shown together with their standard deviations s. Data are divided into the fitting set and test set as used in the parametrization of the GolP-CHARMM force field in J. Chem. Theory Comput. 2013, 9, 1616. Fitting set: Molecule Methane Ethane Butane Hexane Heptane Octane Nonane Ethene 1,3-butadiene Benzene Methanethiol Diethylsulfide Methylamine Imidazole Water

Label CH4 ETH BUT HEX HEP OCT NON ETE BDE BEN MTH DES MAM IMI WTR

N 44 44 47 49 48 48 50 47 50 46 45 47 47 50 49

d (ref) 3.77g / 3.63h 3.84g / 3.64h 3.90g / 3.71h 3.88g / 3.73h 3.72h 3.73h 3.73h 3.35g / 3.17h 3.23h 3.35h 2.88g / 2.91h 3.00g / 2.90h 2.57g / 2.54h 2.51g / 2.52h 3.03g / 2.93h

Label CHX TBU NEN CHE TOL MOH ACT FMA AMM FMN ESH DBS

N 47 45 45 48 45 49 48 49 50 42 47 48

d (ref) 3.71h 3.41h 3.12h 3.25h 3.30h 2.85h 3.00h 3.01h 2.58h 2.78h 2.94h 2.90h

d(min) 3.55 3.66 3.72 3.74 3.74 3.76 3.75 3.18 3.19 3.29 2.61 2.62 2.42 2.37 3.13

d(avr) 3.53 3.62 3.66 3.67 3.68 3.65 3.65 3.18 3.19 3.27 2.60 2.63 2.40 2.36 3.16

s(rms) 0.02 0.02 0.07 0.08 0.07 0.09 0.08 0.02 0.02 0.01 0.03 0.05 0.01 0.01 0.04

d(com) 3.53 3.68 3.82 3.85 3.85 3.90 3.89 3.19 3.21 3.28 2.93 3.35 2.90 3.28 3.19

s(com) 0.02 0.01 0.19 0.11 0.09 0.10 0.09 0.02 0.01 0.01 0.02 0.03 0.01 0.01 0.05

d(avr) 3.74 3.48 3.21 3.31 3.24 2.60 2.69 2.88 2.08 2.62 2.59 2.67

s(rms) 0.01 0.02 0.46 0.02 0.01 0.02 0.04 0.02 0.00 0.03 0.01 0.08

d(com) 3.98 3.52 3.92 3.73 3.35 3.10 3.36 3.18 2.14 3.19 3.15 3.65

s(com) 0.00 0.01 0.32 0.01 0.01 0.02 0.01 0.01 0.00 0.01 0.02 0.08

Test set: Molecule Cyclohexane trans-2-butene Non-1-en Cyclohexene Toluene Methanol Acetone Formic acid Ammonia Formamide Ethanethiol Dibutylsulfide

d(min) 3.72 3.50 3.25 3.30 3.26 2.67 2.69 2.94 2.08 2.63 2.57 2.62

g

plane-wave revPBE-vdW data from J. Chem. Theory Comput. 2013, 9, 1616; hrevPBE-vdW data from this work.

S3

Table S3: Number of adsorbed structures N and adsorption energies [kJ/mol] obtained by revPBEvdW E (ref) and GolP-CHARMM force field for which the lowest-obtained energy E (min), average energy E (avr) and standard deviation s (avr) of average energy are shown. Amino acid Alanine Arginine Asparagine Aspartic acid Cysteine Glutamine Glutamic acid Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine

Label Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

N 39 44 44 37 41 42 44 32 41 45 42 45 42 43 43 37 42 47 46 45

E (ref) -41.3 -112.3 -68.1 -56.8 -59.0 -74.6 -67.1 -60.5 -105.0 -63.4 -61.5 -98.1 -85.6 -86.9 -57.8 -51.1 -59.6 -110.0 -92.6 -57.8

E (min) -49.8 -97.6 -66.7 -62.9 -76.8 -76.3 -78.0 -43.6 -93.0 -67.9 -71.3 -79.1 -92.0 -86.4 -67.6 -54.7 -56.4 -114.2 -94.9 -60.4

E (avr) -48.3 -87.4 -63.1 -60.1 -71.3 -71.0 -70.3 -42.2 -87.4 -62.6 -64.5 -73.3 -86.4 -80.0 -64.2 -50.5 -52.3 -107.5 -87.2 -56.6

s (avr) 1.3 5.7 1.9 2.5 3.9 4.3 5.0 1.5 4.6 4.4 5.6 4.7 5.4 4.0 2.7 3.0 2.4 3.8 9.1 3.7

S4

Table S4: Number of adsorbed structures N and adsorption distances [Å] obtained by revPBEvdW d (ref) and GolP-CHARMM force field for which adsorption distance of the lowest-energy structure d (min), average adsorption distance d (avr) and average distance between surface plane and molecular center of mass d (com) are shown together with their standard deviations s. Amino acid Alanine Arginine Asparagine Aspartic acid Cysteine Glutamine Glutamic acid Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine

Label Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

N 39 44 44 37 41 42 44 32 41 45 42 45 42 43 43 37 42 47 46 45

d (ref) 3.13 2.61 2.72 3.03 3.01 2.79 3.11 2.66 2.62 2.99 3.09 2.60 2.96 3.18 3.08 2.96 2.93 3.22 3.15 3.08

d (min) 2.64 2.71 2.67 2.83 2.59 2.67 2.61 2.73 2.55 2.60 2.97 2.39 2.71 2.88 2.68 2.62 2.82 2.84 2.89 2.64

d (avr) 2.63 2.86 2.64 2.74 2.62 2.66 2.67 2.80 2.56 2.68 2.71 2.50 2.68 2.97 2.69 2.71 2.69 2.99 2.88 2.69

s (rms) 0.03 0.26 0.06 0.08 0.04 0.08 0.05 0.15 0.03 0.08 0.11 0.16 0.06 0.26 0.13 0.10 0.14 0.25 0.17 0.14

d (com) s (com) 3.73 0.04 3.78 0.11 3.63 0.11 3.64 0.15 3.53 0.13 3.69 0.11 3.76 0.19 3.39 0.07 3.71 0.18 3.94 0.12 4.01 0.10 3.75 0.14 3.60 0.13 3.85 0.33 3.66 0.08 3.62 0.11 3.82 0.12 3.72 0.21 3.80 0.53 3.88 0.10

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Ala

Arg

Asn

Asp

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Cys

Gln

Glu

Gly

S7

His

Ile

Leu

Lys

S8

Met

Phe

Pro

Ser

S9

Thr

Trp

Tyr

Val

Figure S1: DFT optimized structures of amino acids adsorbed on Au(111) surface shown in top view (i.e. [111] direction) and side views ([21%0] and [01%1] directions). Gold atoms are shown in orange color while hydrogen, carbon, nitrogen, oxygen and sulfur are colored by white, silver, blue, red and yellow, respectively.

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Figure S2: Sites on Au(111) surface available for molecular adsorption: atop, bridge, hcp hollow and fcc hollow.

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Parameterization of small molecules in GolP-CHARMM Methane Label: Chemical formula:

CH4 CH4

Atomic types and charges: ID 1 2 3 4 5

Atom C H1 H2 H3 H4

Type CT3 HA HA HA HA

Charge -0.360 0.090 0.090 0.090 0.090

Atom C1 H11 H12 H13 C2 H21 H22 H23

Type CT3 HA HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.270 0.090 0.090 0.090

Ethane Label: Chemical formula:

ETH H3C-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8

S12

Butane Label: Chemical formula:

BUT H3C-(CH2)2-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42 H43

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT2 HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090

Hexane Label: Chemical formula:

HEX H3C-(CH2)4-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42

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14 15 16 17 18 19 20

C5 H51 H52 C6 H61 H62 H63

CT2 HA HA CT3 HA HA HA

-0.180 0.090 0.090 -0.270 0.090 0.090 0.090

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62 C7 H71 H72 H73

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

Heptane Label: Chemical formula:

HEP H3C-(CH2)5-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

S14

Octane Label: Chemical formula:

OCT H3C-(CH2)6-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62 C7 H71 H72 C8 H81 H82 H83

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

S15

Nonane Label: Chemical formula:

NON H3C-(CH2)7-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62 C7 H71 H72 C8 H81 H82 C9 H91 H92 H93

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

S16

Ethene Label: Chemical formula:

ETE H2C=CH2

Atomic types and charges: ID 1 2 3 4 5 6

Atom C1 H11 H12 C2 H21 H22

Type CE2 HE2 HE2 CE2 HE2 HE2

Charge -0.420 0.210 0.210 -0.420 0.210 0.210

Type CE2 HE2 HE2 CE1 HE1 CE1 HE1 CE2 HE2 HE2

Charge -0.420 0.210 0.210 -0.150 0.150 -0.150 0.150 -0.420 0.210 0.210

trans-1,3-butadiene Label: Chemical formula:

BDE H2C=CH-CH=CH2

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10

Atom C1 H11 H12 C2 H2 C3 H3 C4 H41 H42

S17

Benzene Label: Chemical formula:

BEN C6H6

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12

Atom C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 C6 H6

Type CA HP CA HP CA HP CA HP CA HP CA HP

Charge -0.115 0.115 -0.115 0.115 -0.115 0.115 -0.115 0.115 -0.115 0.115 -0.115 0.115

Atom C H1 H2 H3 S HS

Type CT3 HA HA HA S HS

Charge -0.201 0.090 0.090 0.090 -0.229 0.160

Methanethiol Label: Chemical formula:

MTH CH3SH

Atomic types and charges: ID 1 2 3 4 5 6

S18

Diethylsulphide Label: Chemical formula:

DES CH3CH2-S-CH2CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Atom C1 H11 H12 H13 C2 H21 H22 S C3 H31 H32 C4 H41 H42 H43

Type CT3 HA HA HA CT2 HA HA S CT2 HA HA CT3 HA HA HA

Charge -0.270 0.090 0.090 0.090 -0.068 0.090 0.090 -0.224 -0.068 0.090 0.090 -0.270 0.090 0.090 0.090

Atom C H1 H2 H3 N HN1 HN2

Type CT3 HA HA HA NHT2 H H

Charge -0.060 0.090 0.090 0.090 -0.990 0.390 0.390

Methylamine Label: Chemical formula:

MAM CH3NH2

Atomic types and charges: ID 1 2 3 4 5 6 7

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Imidazole Label: Chemical formula:

IMI C3N2H4

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9

Atom N1 C1 H1 N2 H2 C3 H3 C4 H4

Type NR2 CPH2 HR1 NR1 H CPH1 HR3 CPH1 HR1

Charge -0.695 0.252 0.124 -0.356 0.312 -0.048 0.090 0.219 0.102

Atom OH2 H1 H2

Type OWT3 HWT3 HWT3

Charge -0.834 0.417 0.417

Atom C1 H11 H12 C2

Type CT2 HA HA CT2

Charge -0.180 0.090 0.090 -0.180

Water Label: Chemical formula:

WTR H2O

Atomic types and charges: ID 1 2 3

Cyclohexane Label: Chemical formula:

CHX C6H12

Atomic types and charges: ID 1 2 3 4

S20

5 6 7 8 9 10 11 12 13 14 15 16 17 18

H21 H22 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62

HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA

0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090

Type CT3 HA HA HA CE1 HE1 CE1 HE1 CT3 HA HA HA

Charge -0.269 0.090 0.090 0.090 -0.151 0.150 -0.151 0.150 -0.269 0.090 0.090 0.090

trans-butene Label: Chemical formula:

TBU H3C-CH=CH-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12

Atom C1 H11 H12 H13 C2 H2 C3 H3 C4 H41 H42 H43

S21

Non-1-en Label: Chemical formula:

NEN H2C=CH-(CH2)6-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

Atom C1 H11 H12 C2 H2 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62 C7 H71 H72 C8 H81 H82 C9 H91 H92 H93

Type CE2 HE2 HE2 CE1 HE1 CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA CT3 HA HA HA

Charge -0.420 0.210 0.210 -0.148 0.150 -0.182 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

S22

Cyclohexene Label: Chemical formula:

CHE C6H10

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

Atom C1 H1 C2 H2 C3 H31 H32 C4 H41 H42 C5 H51 H52 C6 H61 H62

Type CE1 HE1 CE1 HE1 CT2 HA HA CT2 HA HA CT2 HA HA CT2 HA HA

Charge -0.148 0.150 -0.148 0.150 -0.182 0.090 0.090 -0.180 0.090 0.090 -0.180 0.090 0.090 -0.182 0.090 0.090

Atom C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 C6

Type CA HP CA HP CA HP CA HP CA HP CA

Charge -0.116 0.115 -0.114 0.115 -0.115 0.115 -0.114 0.115 -0.116 0.115 -0.001

Toluene Label: Chemical formula:

TOL C6H5-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11

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12 13 14 15

C7 H71 H72 H73

CT3 HA HA HA

-0.269 0.090 0.090 0.090

Atom C H1 H2 H3 O HO

Type CT3 HA HA HA OHM1 H

Charge -0.040 0.090 0.090 0.090 -0.650 0.420

Atom C1 H11 H12 H13 C2 O C3 H31 H32 H33

Type CT3 HA HA HA C O CT3 HA HA HA

Charge -0.229 0.090 0.090 0.090 0.399 -0.481 -0.229 0.090 0.090 0.090

Methanol Label: Chemical formula:

MOH CH3OH

Atomic types and charges: ID 1 2 3 4 5 6

Acetone Label: Chemical formula:

ACT H3C-CO-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10

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Formic acid Label: Chemical formula:

FMA HCOOH

Atomic types and charges: ID 1 2 3 4 5

Atom C H O OH HO

Type CD H OB OH1 H

Charge 0.378 0.112 -0.400 -0.489 0.399

Atom N H1 H2 H3

Type NH3 HC HC HC

Charge -1.125 0.375 0.375 0.375

Atom C H O N HN1 HN2

Type CC HA O NH2 H H

Charge 0.432 0.080 -0.531 -0.681 0.350 0.350

Ammonia Label: Chemical formula:

AMM NH3

Atomic types and charges: ID 1 2 3 4

Formamide Label: Chemical formula:

FMN HCONH2

Atomic types and charges: ID 1 2 3 4 5 6

S25

Ethanethiol Label: Chemical formula:

ESH CH3CH2-SH

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9

Atom C1 H11 H12 H13 C2 H21 H23 S HS

Type CT3 HA HA HA CT2 HA HA S HS

Charge -0.270 0.090 0.090 0.090 -0.109 0.090 0.090 -0.231 0.160

Type CT3 HA HA HA CT2 HA HA CT2 HA HA CT2 HA HA S CT2 HA HA

Charge -0.270 0.090 0.090 0.090 -0.180 0.090 0.090 -0.179 0.090 0.090 -0.060 0.090 0.090 -0.242 -0.060 0.090 0.090

Dibutylsulphide Label: Chemical formula:

DBS H3C-(CH2)3-S-(CH2)3-CH3

Atomic types and charges: ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Atom C1 H11 H12 H13 C2 H21 H22 C3 H31 H32 C4 H41 H42 S C5 H51 H52

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18 19 20 21 22 23 24 25 26 27

C6 H61 H62 C7 H71 H72 C8 H81 H82 H83

CT2 HA HA CT2 HA HA CT3 HA HA HA

-0.179 0.090 0.090 -0.180 0.090 0.090 -0.270 0.090 0.090 0.090

S27

Parameterization of neutral amino acids in GolP-CHARMM Alanine Abbreviation: Chemical formula: Side chain:

Ala (A) C3H7NO2 -CH3

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13

CA HA N H HN C O OH HO CB HB1 HB2 HB3

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT3 -0.270 HA 0.090 HA 0.090 HA 0.090

GolP-CHARMM Type Charge CT1 0.097 HB 0.090 NH2 -0.778 H 0.296 H 0.296 CD 0.752 OH -0.547 OH1 -0.630 H 0.429 CT3 -0.275 HA 0.090 HA 0.090 HA 0.090

Arginine Abbreviation: Chemical formula: Side chain:

Arg (R) C6H14N4O2 -(CH2)3-NH-C(NH)NH2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7

CA HA N H HN C O

CHARMM27 Type Charge CT1 0.070 HB 0.090 HN1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510

GolP-CHARMM Type Charge CT1 0.113 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.723 OB -0.537

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8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

OH HO CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11 HH21 NH2 HH21 HH22

¾ ¾ CT2 HA HA CT2 HA HA CT2 HA HA NC2 HC CG NC2 HC HC NC2 HC HC

¾ ¾ -0.180 0.090 0.090 -0.180 0.090 0.090 0.200 0.090 0.090 -0.700 0.440 0.640 -0.800 0.460 0.460 -0.800 0.460 0.460

OH1 H CT2 HA HA CT2 HA HA CT2 HA HA NC2 HC CG NC2 HC ¾ NC2 HC HC

-0.632 0.429 -0.182 0.090 0.090 -0.173 0.090 0.090 0.198 0.090 0.090 -0.777 0.440 0.619 -0.777 0.296 ¾ -0.777 0.296 0.296

Asparagine Abbreviation: Chemical formula: Side chain:

Asn (N) C4H8N2O3 -CH2-CONH2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14

CA HA N H HN C O OH HO CB HB2 HB3 CG OD1

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CC 0.550 O -0.550

GolP-CHARMM Type Charge CT1 0.112 HB 0.090 NH2 -0.774 H 0.296 H 0.296 CD 0.720 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.177 HA 0.090 HA 0.090 CC 0.547 O -0.551

S29

15 16 17

ND2 HD21 HD22

NH2 H H

-0.620 0.320 0.300

NH2 H H

-0.619 0.310 0.310

Aspartic acid Abbreviation: Chemical formula: Side chain:

Asp (D) C4H7NO4 -CH2-COOH

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

CA HA N H HN C O OH HO CB HB2 HB3 CG OD1 OD2 HD

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.280 HA 0.090 HA 0.090 CC 0.620 OC -0.760 OC -0.760 ¾ ¾

GolP-CHARMM Type Charge CT1 0.116 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.720 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.202 HA 0.090 HA 0.090 CD 0.800 OB -0.576 OH1 -0.632 H 0.429

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470

GolP-CHARMM Type Charge CT1 0.115 HB 0.090 NH2 -0.777

Cysteine Abbreviation: Chemical formula: Side chain:

Cys (C) C3H7NO2S -CH2-SH

Atomic types and charges: ID

Atom

1 2 3

CA HA N

S30

4 5 6 7 8 9 10 11 12 13 14

H HN C O OH HO CB HB2 HB3 SG HG

H ¾ C O ¾ ¾ CT2 HA HA S HS

0.310 ¾ 0.510 -0.510 ¾ ¾ -0.110 0.090 0.090 -0.230 0.160

H H CD OB OH1 H CT2 HA HA ST HS

0.296 0.296 0.720 -0.537 -0.632 0.429 -0.099 0.090 0.090 -0.241 0.160

Glutamic acid Abbreviation: Chemical formula: Side chain:

Glu (E) C5H9NO4 -(CH2)2-COOH

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

CA HA N H HN C O OH HO CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 HE

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.410 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CT2 -0.280 HA 0.090 HA 0.090 CC 0.620 OC -0.760 OC -0.760 ¾ ¾

GolP-CHARMM Type Charge CT1 0.120 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.723 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.171 HA 0.090 HA 0.090 CT2 -0.220 HA 0.090 HA 0.090 CD 0.802 OB -0.576 OH1 -0.632 H 0.429

S31

Glutamine Abbreviation: Chemical formula: Side chain:

Gln (Q) C5H10N2O3 -(CH2)2-CONH2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

CA HA N H HN C O OH HO CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21 HE22

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CT2 -0.180 HA 0.090 HA 0.090 CC 0.550 O -0.550 NH2 -0.620 H 0.320 H 0.300

GolP-CHARMM Type Charge CT1 0.118 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.723 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.182 HA 0.090 HA 0.090 CT2 -0.181 HA 0.090 HA 0.090 CC 0.544 O -0.544 NH2 -0.623 H 0.310 H 0.310

CHARMM27 Type Charge CT2 -0.020 HB 0.090 NH1 -0.470 H 0.310

GolP-CHARMM Type Charge CT2 0.100 HB 0.090 NH2 -0.956 H 0.338

Glycine Abbreviation: Chemical formula: Side chain:

Gly (G) C2H5NO2 -H

Atomic types and charges: ID

Atom

1 2 3 4

CA HA2 N H

S32

5 6 7 8 9 10

HN C O OH HO HA3

¾ C O ¾ ¾ HB

¾ 0.510 -0.510 ¾ ¾ 0.090

H CD OB OH1 H HB

0.338 0.751 -0.551 -0.629 0.429 0.090

Histidine Abbreviation: Chemical formula: Side chain:

His (H) C6H9N3O2 -CH2-C3N2H3

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

CA HA N H HN C O OH HO CB HB2 HB3 CG ND1 CE1 HE1 NE2 HE2 CD2 HD2

CHARMM27 Type Charge CT1 0.070 HB 0.310 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.080 HA 0.090 HA 0.090 CPH1 0.220 NR1 -0.700 CPH2 0.250 HR1 0.130 NR1 -0.360 H 0.320 CPH1 -0.050 HR3 0.090

GolP-CHARMM Type Charge CT1 0.118 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.719 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.079 HA 0.090 HA 0.090 CPH1 0.219 NR2 -0.696 CPH2 0.252 HR1 0.124 NR1 -0.356 H 0.312 CPH1 -0.048 HR3 0.090

S33

Isoleucine Abbreviation: Chemical formula: Side chain:

Ile (I) C6H13NO2 -CH(CH3)-CH2-CH3

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

CA HA N H HN C O OH HO CB HB CG2 HG21 HG22 HG23 CG1 HG12 HG13 CD HD1 HD2 HD3

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT1 -0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090 CT2 -0.180 HA 0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090

GolP-CHARMM Type Charge CT1 0.098 HB 0.090 NH2 -0.772 H 0.296 H 0.296 CD 0.736 OB -0.537 OH1 -0.632 H 0.429 CT1 -0.094 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090 CT2 -0.181 HA 0.090 HA 0.090 CT3 -0.269 HA 0.090 HA 0.090 HA 0.090

S34

Leucine Abbreviation: Chemical formula: Side chain:

Leu (L) C6H13NO2 -CH2-CH(CH3)2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

CA HA N H HN C O OH HO CB HB2 HB3 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CT1 -0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090

GolP-CHARMM Type Charge CT1 0.115 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.720 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.176 HA 0.090 HA 0.090 CT1 -0.088 HA 0.090 CT3 -0.273 HA 0.090 HA 0.090 HA 0.090 CT3 -0.273 HA 0.090 HA 0.090 HA 0.090

S35

Lysine Abbreviation: Chemical formula: Side chain:

Lys (K) C6H14N2O2 -(CH2)4-NH2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

CA HA N H HN C O OH HO CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CT2 -0.180 HA 0.090 HA 0.090 CT2 -0.180 HA 0.090 HA 0.090 CT2 0.210 HA 0.050 HA 0.050 NH3 -0.300 HC 0.330 HC 0.330 HC 0.330

GolP-CHARMM Type Charge CT1 0.119 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.723 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.183 HA 0.090 HA 0.090 CT2 -0.216 HA 0.090 HA 0.090 CT2 -0.153 HA 0.090 HA 0.090 CT2 0.008 HA 0.090 HA 0.090 NHT2 -0.775 HC 0.296 HC 0.296 ¾ ¾

S36

Methionine Abbreviation: Chemical formula: Side chain:

Met (M) C5H11NO2S -(CH2)2-S-CH3

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

CA HA N H HN C O OH HO CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CT2 -0.140 HA 0.090 HA 0.090 S -0.090 CT3 -0.220 HA 0.090 HA 0.090 HA 0.090

GolP-CHARMM Type Charge CT1 0.112 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.723 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.182 HA 0.090 HA 0.090 CT2 -0.125 HA 0.090 HA 0.090 S -0.103 CT3 -0.220 HA 0.090 HA 0.090 HA 0.090

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310

GolP-CHARMM Type Charge CT1 0.114 HB 0.090 NH2 -0.778 H 0.296

Phenylalanine Abbreviation: Chemical formula: Side chain:

Phe (F) C9H11NO2 -CH2-C6H5

Atomic types and charges: ID

Atom

1 2 3 4

CA HA N H

S37

5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

HN C O OH HO CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2

¾ C O ¾ ¾ CT2 HA HA CA CA HP CA HP CA HP CA HP CA HP

¾ 0.510 -0.510 ¾ ¾ -0.180 0.090 0.090 0.000 -0.115 0.115 -0.115 0.115 -0.115 0.115 -0.115 0.115 -0.115 0.115

H CD OB OH1 H CT2 HA HA CA CA HP CA HP CA HP CA HP CA HP

0.296 0.718 -0.537 -0.632 0.429 -0.179 0.090 0.090 -0.005 -0.118 0.115 -0.108 0.115 -0.115 0.115 -0.108 0.115 -0.118 0.115

Proline Abbreviation: Chemical formula: Side chain:

Pro (P) C5H9NO2 -(CH2)3-

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

CA HA C O OH HO N HN CD HD2 HD3 CG HG2 HG3 CB

CHARMM27 Type Charge CP1 0.020 HB 0.090 C 0.510 O -0.510 ¾ ¾ ¾ ¾ N -0.290 ¾ ¾ CP3 0.000 HA 0.090 HA 0.090 CP2 -0.180 HA 0.090 HA 0.090 CP2 -0.180

GolP-CHARMM Type Charge CP1 0.215 HB 0.090 CD 0.737 OB -0.570 OH1 -0.632 H 0.429 NH1 -0.851 H 0.361 CP3 0.101 HA 0.090 HA 0.090 CP2 -0.211 HA 0.090 HA 0.090 CP2 -0.209

S38

16 17

HB2 HB3

HA HA

0.090 0.090

HA HA

0.090 0.090

Serine Abbreviation: Chemical formula: Side chain:

Ser (S) C3H7NO3 -CH2-OH

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14

CA HA N H HN C O OH HO CB HB2 HB3 OG HG

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 0.050 HA 0.090 HA 0.090 OH1 -0.660 H 0.430

GolP-CHARMM Type Charge CT1 0.113 HB 0.090 NH2 -0.776 H 0.296 H 0.296 CD 0.720 OB -0.537 OH1 -0.632 H 0.429 CT2 0.050 HA 0.090 HA 0.090 OHM1 -0.649 H 0.420

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510

GolP-CHARMM Type Charge CT1 0.100 HB 0.090 NH2 -0.775 H 0.296 H 0.296 CD 0.737

Threonine Abbreviation: Chemical formula: Side chain:

Thr (T) C4H9NO3 -CH(OH)-CH3

Atomic types and charges: ID

Atom

1 2 3 4 5 6

CA HA N H NH C

S39

7 8 9 10 11 12 13 14 15 16 17

O OH HO CB HB OG1 HG1 CG2 HG21 HG22 HG23

O ¾ ¾ CT1 HA OH1 H CT3 HA HA HA

-0.510 ¾ ¾ 0.140 0.090 -0.660 0.430 -0.270 0.090 0.090 0.090

OB OH1 H CT1 HA OHM1 H CT3 HA HA HA

-0.537 -0.632 0.429 0.140 0.090 -0.651 0.419 -0.272 0.090 0.090 0.090

Tryptophan Abbreviation: Chemical formula: Side chain:

Trp (W) C11H12N2O2 -CH2-C8NH6

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

CA HA N H HN C O OH HO CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CY -0.030 CA 0.035 HP 0.115 NY -0.610 H 0.380 CPT 0.130 CA -0.115 HP 0.115 CA -0.115 HP 0.115 CA -0.115

GolP-CHARMM Type Charge CT1 0.108 HB 0.090 NH2 -0.777 H 0.296 H 0.296 CD 0.719 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.188 HA 0.090 HA 0.090 CY -0.042 CA -0.156 HP 0.220 NY -0.521 H 0.363 CPT 0.235 CA -0.282 HP 0.193 CA -0.196 HP 0.196 CA -0.237

S40

24 25 26 27

HZ3 CE3 HE3 CD2

HP CA HP CPT

0.115 -0.115 0.115 -0.020

HP CA HP CPT

0.196 -0.255 0.199 0.103

Tyrosine Abbreviation: Chemical formula: Side chain:

Tys (Y) C9H11N2O3 -CH2-C6H4-OH

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

CA HA N H HN C O OH HO CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT2 -0.180 HA 0.090 HA 0.090 CA 0.000 CA -0.115 HP 0.115 CA -0.115 HP 0.115 CA 0.110 OH1 -0.540 H 0.410 CA -0.115 HP 0.115 CA -0.115 HP 0.115

GolP-CHARMM Type Charge CT1 0.114 HB 0.090 NH2 -0.778 H 0.296 H 0.296 CD 0.718 OB -0.537 OH1 -0.632 H 0.429 CT2 -0.179 HA 0.090 HA 0.090 CA -0.005 CA -0.115 HP 0.115 CA -0.110 HP 0.115 CA 0.108 OH1 -0.530 H 0.420 CA -0.110 HP 0.115 CA -0.115 HP 0.115

S41

Valine Abbreviation: Chemical formula: Side chain:

Val (V) C5H11NO2 -CH(CH3)2

Atomic types and charges: ID

Atom

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

CA HA N H NH C O OH HO CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23

CHARMM27 Type Charge CT1 0.070 HB 0.090 NH1 -0.470 H 0.310 ¾ ¾ C 0.510 O -0.510 ¾ ¾ ¾ ¾ CT1 -0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090 CT3 -0.270 HA 0.090 HA 0.090 HA 0.090

GolP-CHARMM Type Charge CT1 0.099 HB 0.090 NH2 -0.772 H 0.296 H 0.296 CD 0.736 OB -0.537 OH1 -0.632 H 0.429 CT1 -0.089 HA 0.090 CT3 -0.273 HA 0.090 HA 0.090 HA 0.090 CT3 -0.273 HA 0.090 HA 0.090 HA 0.090

S42