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‎input_files/cd-set1/README.md‎

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## CD Set 1: Experimental binding free energy and binding enthalpy
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Guest ID labels with 's' (e.g., s9) indicate supplementary guests to the core set listed in the associated paper. All values in kcal/mol.
2+
Guest ID labels with 's' (e.g., s9) indicate supplementary guests to the core set listed in the associated paper. All values in kcal/mol. The guest names and SMILES strings reflect the expected protonation state at pH 6.9, and thus differ from those in the manuscript which reflect the unionized state.
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|Host|Guest |Guest ID|Exp ΔG [<sup>a</sup>](#Rek97)|Exp ΔG SEM [<sup>a</sup>](#Rek97)|Exp ΔH [<sup>a</sup>](#Rek97)|Exp ΔH SEM [<sup>a</sup>](#Rek97)|Comp. Studies|
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|----|--------------------------|--------|------|----------|------|----------|-------------|
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|aCD |1-butylamine | 1|-1.575|0.019 | -2.17|0.05 | [1](#HenGil)|
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|aCD |1-hexylamine | 2|-3.533|0.004 | -4.19|0.02 | [1](#HenGil)|
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|aCD |1-octylamine | 3|-4.606|0.007 | -5.46|0.03 | [1](#HenGil)|
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|aCD |cyclopentanol | 4|-2.130|0.016 | -2.74|0.02 | [1](#HenGil)|
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|aCD |cycloheptanol | 5|-2.510|0.060 | -2.99|0.23 | [1](#HenGil)|
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|aCD |butanoate | 6|-1.506|0.036 | -2.53|0.12 | [1](#HenGil)|
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|aCD |hexanoate | 7|-3.380|0.005 | -3.40|0.02 | [1](#HenGil)|
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|aCD |octanoate | 8|-4.622|0.017 | -4.89|0.03 | [1](#HenGil)|
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|Host|Guest|Guest ID|Guest SMILES|Exp ΔG [<sup>a</sup>](#Rek97)|Exp ΔG SEM [<sup>a</sup>](#Rek97)|Exp ΔH [<sup>a</sup>](#Rek97)|Exp ΔH SEM [<sup>a</sup>](#Rek97)|Comp. Studies|
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|----|--------------------------|--------|-----------------------|------|----------|------|----------|-------------|
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|aCD |1-butylammonium |1 |CCCC[NH3+] |-1.575|0.019 | -2.17|0.05 | [1](#HenGil)|
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|aCD |1-hexylammonium |2 |CCCCCC[NH3+] |-3.533|0.004 | -4.19|0.02 | [1](#HenGil)|
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|aCD |1-octylammonium |3 |CCCCCCCC[NH3+] |-4.606|0.007 | -5.46|0.03 | [1](#HenGil)|
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|aCD |cyclopentanol |4 |OC1CCCC1 |-2.130|0.016 | -2.74|0.02 | [1](#HenGil)|
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|aCD |cycloheptanol |5 |OC1CCCCCC1 |-2.510|0.060 | -2.99|0.23 | [1](#HenGil)|
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|aCD |butanoate |6 |CCCC([O-])=O |-1.506|0.036 | -2.53|0.12 | [1](#HenGil)|
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|aCD |hexanoate |7 |CCCCCC([O-])=O |-3.380|0.005 | -3.40|0.02 | [1](#HenGil)|
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|aCD |octanoate |8 |CCCCCCCC([O-])=O |-4.622|0.017 | -4.89|0.03 | [1](#HenGil)|
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||
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|aCD |n-methylbutylamine | s9|-1.685|0.018 | -2.57|0.06 | [1](#HenGil)|
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|aCD |1-methylbutylamine | s10|-1.764|0.020 | -2.68|0.07 | [1](#HenGil)|
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|aCD |1-pentylamine | s11|-2.720|0.004 | -3.28|0.02 | [1](#HenGil)|
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|aCD |n-methylhexylamine | s12|-3.516|0.012 | -4.20|0.08 | [1](#HenGil)|
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|aCD |1-methylhexylamine | s13|-3.604|0.004 | -4.28|0.02 | [1](#HenGil)|
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|aCD |1-heptylamine | s14|-4.137|0.004 | -4.66|0.02 | [1](#HenGil)|
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|aCD |1-methylheptylamine | s15|-4.166|0.004 | -4.74|0.02 | [1](#HenGil)|
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|aCD |cyclobutanol | s16|-2.022|0.016 | -2.75|0.05 | [1](#HenGil)|
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|aCD |cyclooctanol | s17|-3.227|1.135 | -0.93|0.32 | [1](#HenGil)|
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|aCD |pentanoate | s18|-2.596|0.005 | -2.75|0.01 | [1](#HenGil)|
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|aCD |trans-2-hexenoate | s19|-3.344|0.010 | -4.12|0.06 | [1](#HenGil)|
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|aCD |trans-3-hexenoate | s20|-3.011|0.010 | -3.36|0.05 | [1](#HenGil)|
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|aCD |heptanoate | s21|-3.991|0.013 | -4.19|0.09 | [1](#HenGil)|
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|aCD |6-heptenoate | s22|-3.597|0.004 | -4.48|0.02 | [1](#HenGil)|
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|aCD |n-methylbutylammonium |s9 |CCCC[NH2+]C |-1.685|0.018 | -2.57|0.06 | [1](#HenGil)|
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|aCD |1-methylbutylammonium |s10 |CCCC(C)[NH3+] |-1.764|0.020 | -2.68|0.07 | [1](#HenGil)|
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|aCD |1-pentylammonium |s11 |CCCCC[NH3+] |-2.720|0.004 | -3.28|0.02 | [1](#HenGil)|
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|aCD |n-methylhexylammonium |s12 |CCCCCC[NH2+]C |-3.516|0.012 | -4.20|0.08 | [1](#HenGil)|
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|aCD |1-methylhexylammonium |s13 |CCCCCC(C)[NH3+] |-3.604|0.004 | -4.28|0.02 | [1](#HenGil)|
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|aCD |1-heptylammonium |s14 |CCCCCCC[NH3+] |-4.137|0.004 | -4.66|0.02 | [1](#HenGil)|
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|aCD |1-methylheptylammonium |s15 |CCCCCCC(C)[NH3+] |-4.166|0.004 | -4.74|0.02 | [1](#HenGil)|
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|aCD |cyclobutanol |s16 |OC1CCC1 |-2.022|0.016 | -2.75|0.05 | [1](#HenGil)|
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|aCD |cyclooctanol |s17 |OC1CCCCCCC1 |-3.227|1.135 | -0.93|0.32 | [1](#HenGil)|
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|aCD |pentanoate |s18 |CCCCC([O-])=O |-2.596|0.005 | -2.75|0.01 | [1](#HenGil)|
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|aCD |trans-2-hexenoate |s19 |CCC/C=C/C([O-])=O |-3.344|0.010 | -4.12|0.06 | [1](#HenGil)|
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|aCD |trans-3-hexenoate |s20 |CC/C=C/CC([O-])=O |-3.011|0.010 | -3.36|0.05 | [1](#HenGil)|
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|aCD |heptanoate |s21 |CCCCCCC([O-])=O |-3.991|0.013 | -4.19|0.09 | [1](#HenGil)|
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|aCD |6-heptenoate |s22 |[O-]C(=O)CCCCC=C |-3.597|0.004 | -4.48|0.02 | [1](#HenGil)|
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<a name="Rek97"></a>a) Experimental Data: Rekharsky MV, Mayhew MP, Goldberg RN, Ross PD, Yamashoji Y, Inoue Y. (1997) Thermodynamic and nuclear magnetic resonance study of the reactions of α-and β-cyclodextrin with acids, aliphatic amines, and cyclic alcohols. J Phys Chem B. 101(1):87-100. doi: 10.1021/jp962715n
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a) <a name="Rek97"></a> Experimental Data: Rekharsky MV, Mayhew MP, Goldberg RN, Ross PD, Yamashoji Y, Inoue Y. (1997) Thermodynamic and nuclear magnetic resonance study of the reactions of α-and β-cyclodextrin with acids, aliphatic amines, and cyclic alcohols. J Phys Chem B. 101(1):87-100. doi: 10.1021/jp962715n
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Computational Studies:
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<a name="HenGil"></a>1) Niel M. Henriksen and Michael K. Gilson. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. Journal of Chemical Theory and Computation. Article ASAP. DOI: 10.1021/acs.jctc.7b00359
33+
1. <a name="HenGil"></a> Niel M. Henriksen and Michael K. Gilson. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. Journal of Chemical Theory and Computation. Article ASAP. DOI: 10.1021/acs.jctc.7b00359

‎input_files/cd-set2/README.md‎

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## CD Set 2: Experimental binding free energy and binding enthalpy
2-
Guest ID labels with 's' (e.g., s13) indicate supplementary guests to the core set listed in the associated paper. All values in kcal/mol.
2+
Guest ID labels with 's' (e.g., s13) indicate supplementary guests to the core set listed in the associated paper. All values in kcal/mol. The guest names and SMILES strings reflect the expected protonation state at pH 6.9, and thus differ from those in the manuscript which reflect the unionized state.
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|Host|Guest |Guest ID|Exp ΔG [<sup>a</sup>](#Rek97)|Exp ΔG SEM [<sup>a</sup>](#Rek97)|Exp ΔH [<sup>a</sup>](#Rek97)|Exp ΔH SEM [<sup>a</sup>](#Rek97)|Comp. Studies|
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|----|--------------------------|--------|------|----------|------|----------|-------------|
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|bCD |1-hexylamine | 1|-2.486|0.084 | 0.60|0.05 | [1](#HenGil)|
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|bCD |1-octylamine | 2|-3.585|0.120 | -0.48|0.03 | [1](#HenGil)|
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|bCD |cyclopentanol | 3|-3.050|0.010 | -1.09|0.01 | [1](#HenGil)|
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|bCD |trans-4-methylcyclohexanol| 4|-4.541|0.008 | -2.17|0.02 | [1](#HenGil)|
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|bCD |cycloheptanol | 5|-4.560|0.011 | -2.96|0.01 | [1](#HenGil)|
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|bCD |pentanoate | 6|-1.267|0.323 | 1.89|0.53 | [1](#HenGil)|
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|bCD |heptanoate | 7|-3.394|0.179 | 0.42|0.04 | [1](#HenGil)|
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|bCD |benzoate | 8|-1.640|0.024 | -2.51|0.08 | [1](#HenGil)|
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|bCD |phenylacetate | 9|-1.697|0.048 | -1.79|0.11 | [1](#HenGil)|
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|bCD |4-methylphenylacetate | 10|-2.192|0.013 | -2.89|0.05 | [1](#HenGil)|
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|bCD |4-methoxyphenylacetate | 11|-2.512|0.007 | -1.96|0.01 | [1](#HenGil)|
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|bCD |4-phenylbutanoate | 12|-3.599|0.018 | -2.82|0.01 | [1](#HenGil)|
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| Supplemental Guest Data
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|bCD |1-methylhexylamine | s13|-2.557|0.066 | 0.47|0.03 | [1](#HenGil)|
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|bCD |cyclobutanol | s14|-1.554|0.167 | 0.88|0.17 | [1](#HenGil)|
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|bCD |1-methylcyclohexanol | s15|-4.175|0.010 | -2.29|0.03 | [1](#HenGil)|
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|bCD |cis-4-methylcyclohexanol | s16|-4.319|0.006 | -2.27|0.01 | [1](#HenGil)|
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|bCD |cyclooctanol | s17|-4.971|0.036 | -3.92|0.06 | [1](#HenGil)|
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|bCD |hexanoate | s18|-2.280|0.030 | 1.31|0.04 | [1](#HenGil)|
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|bCD |3-methylphenylacetate | s19|-1.458|0.036 | -2.75|0.13 | [1](#HenGil)|
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|bCD |3-methoxyphenylacetate | s20|-2.156|0.010 | -2.93|0.03 | [1](#HenGil)|
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|bCD |3-phenylbutanoate | s21|-3.518|0.007 | -2.25|0.01 | [1](#HenGil)|
4+
|Host|Guest|Guest ID|Guest SMILES|Exp ΔG [<sup>a</sup>](#Rek97)|Exp ΔG SEM [<sup>a</sup>](#Rek97)|Exp ΔH [<sup>a</sup>](#Rek97)|Exp ΔH SEM [<sup>a</sup>](#Rek97)|Comp. Studies|
5+
|----|--------------------------|--------|-----------------------|------|----------|------|----------|-------------|
6+
|bCD |1-hexylammonium |1 |CCCCCC[NH3+] |-2.486|0.084 | 0.60|0.05 | [1](#HenGil)|
7+
|bCD |1-octylammonium |2 |CCCCCCCC[NH3+] |-3.585|0.120 | -0.48|0.03 | [1](#HenGil)|
8+
|bCD |cyclopentanol |3 |OC1CCCC1 |-3.050|0.010 | -1.09|0.01 | [1](#HenGil)|
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|bCD |trans-4-methylcyclohexanol|4 |C[C@@H]1CC[C@@H](O)CC1 |-4.541|0.008 | -2.17|0.02 | [1](#HenGil)|
10+
|bCD |cycloheptanol |5 |OC1CCCCCC1 |-4.560|0.011 | -2.96|0.01 | [1](#HenGil)|
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|bCD |pentanoate |6 |CCCCC([O-])=O |-1.267|0.323 | 1.89|0.53 | [1](#HenGil)|
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|bCD |heptanoate |7 |CCCCCCC([O-])=O |-3.394|0.179 | 0.42|0.04 | [1](#HenGil)|
13+
|bCD |benzoate |8 |[O-]C(=O)c1ccccc1 |-1.640|0.024 | -2.51|0.08 | [1](#HenGil)|
14+
|bCD |phenylacetate |9 |[O-]C(=O)Cc1ccccc1 |-1.697|0.048 | -1.79|0.11 | [1](#HenGil)|
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|bCD |4-methylphenylacetate |10 |Cc1ccc(CC([O-])=O)cc1 |-2.192|0.013 | -2.89|0.05 | [1](#HenGil)|
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|bCD |4-methoxyphenylacetate |11 |COc1ccc(CC([O-])=O)cc1 |-2.512|0.007 | -1.96|0.01 | [1](#HenGil)|
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|bCD |4-phenylbutanoate |12 |[O-]C(=O)CCCc1ccccc1 |-3.599|0.018 | -2.82|0.01 | [1](#HenGil)|
18+
||
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|bCD |1-methylhexylammonium |s13 |CCCCCC(C)[NH3+] |-2.557|0.066 | 0.47|0.03 | [1](#HenGil)|
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|bCD |cyclobutanol |s14 |OC1CCC1 |-1.554|0.167 | 0.88|0.17 | [1](#HenGil)|
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|bCD |1-methylcyclohexanol |s15 |CC1(O)CCCCC1 |-4.175|0.010 | -2.29|0.03 | [1](#HenGil)|
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|bCD |cis-4-methylcyclohexanol |s16 |C[C@H]1CC[C@@H](O)CC1 |-4.319|0.006 | -2.27|0.01 | [1](#HenGil)|
23+
|bCD |cyclooctanol |s17 |OC1CCCCCCC1 |-4.971|0.036 | -3.92|0.06 | [1](#HenGil)|
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|bCD |hexanoate |s18 |CCCCCC([O-])=O |-2.280|0.030 | 1.31|0.04 | [1](#HenGil)|
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|bCD |3-methylphenylacetate |s19 |Cc1cccc(CC([O-])=O)c1 |-1.458|0.036 | -2.75|0.13 | [1](#HenGil)|
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|bCD |3-methoxyphenylacetate |s20 |COc1cccc(CC([O-])=O)c1 |-2.156|0.010 | -2.93|0.03 | [1](#HenGil)|
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|bCD |3-phenylbutanoate |s21 |CC(CC([O-])=O)c1ccccc1 |-3.518|0.007 | -2.25|0.01 | [1](#HenGil)|
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29-
<a name="Rek97"></a>a) Experimental Data: Rekharsky MV, Mayhew MP, Goldberg RN, Ross PD, Yamashoji Y, Inoue Y. (1997) Thermodynamic and nuclear magnetic resonance study of the reactions of α-and β-cyclodextrin with acids, aliphatic amines, and cyclic alcohols. J Phys Chem B. 101(1):87-100. doi: 10.1021/jp962715n
29+
a) <a name="Rek97"></a>Experimental Data: Rekharsky MV, Mayhew MP, Goldberg RN, Ross PD, Yamashoji Y, Inoue Y. (1997) Thermodynamic and nuclear magnetic resonance study of the reactions of α-and β-cyclodextrin with acids, aliphatic amines, and cyclic alcohols. J Phys Chem B. 101(1):87-100. doi: 10.1021/jp962715n
3030

3131
Computational Studies:
32-
<a name="HenGil"></a>1) Niel M. Henriksen and Michael K. Gilson. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. Journal of Chemical Theory and Computation. Article ASAP. DOI: 10.1021/acs.jctc.7b00359
32+
1. <a name="HenGil"></a>Niel M. Henriksen and Michael K. Gilson. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. Journal of Chemical Theory and Computation. Article ASAP. DOI: 10.1021/acs.jctc.7b00359
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