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Added references to other computational studies
The Zhang 2016 paper has a bunch more of the same guests, but they were all treated as neutral, whereas the experiment had the guests charged. I've omitted them to avoid confusion. Also, I just realized that names like "4-methylphenylacetate" may have caused confusion in the literature. Rekharsky 1997 used that name to refer to the charged version of 4-methylphenylacetic acid, but both Wickstrom 2013 or Zhang 2016 interpreted it as the structure that is more commonly known as "p-tolyl acetate" which is totally different. This occurred for several different related compounds. I've left those off the list as well, because clearly the numbers won't be comparable.
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‎input_files/cd-set2/README.md‎

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@@ -3,31 +3,36 @@ Guest ID labels with 's' (e.g., s13) indicate supplementary guests to the core s
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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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|bCD |1-hexylammonium |1 |CCCCCC[NH3+] |-2.486|0.084 | 0.60|0.05 | [1](#HenGil)|
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|bCD |1-octylammonium |2 |CCCCCCCC[NH3+] |-3.585|0.120 | -0.48|0.03 | [1](#HenGil)|
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|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)|
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|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)|
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|bCD |benzoate |8 |[O-]C(=O)c1ccccc1 |-1.640|0.024 | -2.51|0.08 | [1](#HenGil)|
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|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)|
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|bCD |1-hexylammonium |1 |CCCCCC[NH3+] |-2.486|0.084 | 0.60|0.05 | [1](#Hen17),[2](#Wic13)|
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|bCD |1-octylammonium |2 |CCCCCCCC[NH3+] |-3.585|0.120 | -0.48|0.03 | [1](#Hen17)|
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|bCD |cyclopentanol |3 |OC1CCCC1 |-3.050|0.010 | -1.09|0.01 | [1](#Hen17),[2](#Wic13),[3](#Zha16)|
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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](#Hen17),[2](#Wic13)|
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|bCD |cycloheptanol |5 |OC1CCCCCC1 |-4.560|0.011 | -2.96|0.01 | [1](#Hen17),[2](#Wic13),[3](#Zha16)|
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|bCD |pentanoate |6 |CCCCC([O-])=O |-1.267|0.323 | 1.89|0.53 | [1](#Hen17)|
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|bCD |heptanoate |7 |CCCCCCC([O-])=O |-3.394|0.179 | 0.42|0.04 | [1](#Hen17)|
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|bCD |benzoate |8 |[O-]C(=O)c1ccccc1 |-1.640|0.024 | -2.51|0.08 | [1](#Hen17)|
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|bCD |phenylacetate |9 |[O-]C(=O)Cc1ccccc1 |-1.697|0.048 | -1.79|0.11 | [1](#Hen17)|
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|bCD |4-methylphenylacetate |10 |Cc1ccc(CC([O-])=O)cc1 |-2.192|0.013 | -2.89|0.05 | [1](#Hen17)|
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|bCD |4-methoxyphenylacetate |11 |COc1ccc(CC([O-])=O)cc1 |-2.512|0.007 | -1.96|0.01 | [1](#Hen17)|
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|bCD |4-phenylbutanoate |12 |[O-]C(=O)CCCc1ccccc1 |-3.599|0.018 | -2.82|0.01 | [1](#Hen17)|
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||
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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)|
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|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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|bCD |1-methylhexylammonium |s13 |CCCCCC(C)[NH3+] |-2.557|0.066 | 0.47|0.03 | [1](#Hen17)|
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|bCD |cyclobutanol |s14 |OC1CCC1 |-1.554|0.167 | 0.88|0.17 | [1](#Hen17),[2](#Wic13)|
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|bCD |1-methylcyclohexanol |s15 |CC1(O)CCCCC1 |-4.175|0.010 | -2.29|0.03 | [1](#Hen17),[2](#Wic13),[3](#Zha16)|
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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](#Hen17)|
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|bCD |cyclooctanol |s17 |OC1CCCCCCC1 |-4.971|0.036 | -3.92|0.06 | [1](#Hen17),[2](#Wic13),[3](#Zha16)|
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|bCD |hexanoate |s18 |CCCCCC([O-])=O |-2.280|0.030 | 1.31|0.04 | [1](#Hen17)|
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|bCD |3-methylphenylacetate |s19 |Cc1cccc(CC([O-])=O)c1 |-1.458|0.036 | -2.75|0.13 | [1](#Hen17)|
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|bCD |3-methoxyphenylacetate |s20 |COc1cccc(CC([O-])=O)c1 |-2.156|0.010 | -2.93|0.03 | [1](#Hen17)|
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|bCD |3-phenylbutanoate |s21 |CC(CC([O-])=O)c1ccccc1 |-3.518|0.007 | -2.25|0.01 | [1](#Hen17)|
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a) <a name="Rek97"></a> Experimental Data: Rekharsky, M. V.; Mayhew, M. P.; Goldberg, R. N.; Ross, P. D.; Yamashoji, Y.; Inoue, Y. 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 1997, 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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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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1. <a name="Hen17"></a> Henriksen, N. M.; Gilson, M. K. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. J. Chem. Theory Comput. 2017 DOI: 10.1021/acs.jctc.7b00359.
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2. <a name="Wic13"></a> Wickstrom, L.; He, P.; Gallicchio, E.; Levy, R. M. Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process. J. Chem. Theory Comput. 2013, 9 (7), 3136–3150 DOI: 10.1021/ct400003r.
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3. <a name="Zha16"></a> Zhang, H.; Yin, C.; Yan, H.; van der Spoel, D. Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host–Guest Complexes. J. Chem. Inf. Model. 2016 DOI: 10.1021/acs.jcim.6b00418.
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