updated theory section

paper/alchemical.bib

@@ -4549,4 +4549,140 @@ @article{zwanzig1954hightemperature
   file = {/Users/toni_brain/Zotero/storage/SR4C6RM8/GetabsServlet.html},
   journal = {J. Chem. Phys.},
   number = {8}
+}
+
+@article{gilson2007calculation,
+  title={Calculation of protein-ligand binding affinities},
+  author={Gilson, Michael K and Zhou, Huan-Xiang},
+  journal={Annu. Rev. Biophys. Biomol. Struct.},
+  volume={36},
+  number={1},
+  pages={21--42},
+  doi = {10.1146/annurev.biophys.36.040306.132550},
+  year={2007},
+  publisher={Annual Reviews}
+}
+
+
+
+@InBook{guggenheim1952mixtures504,
+  author = 	 {Guggenheim, E. A.},
+  title = 	 {Mixtures},
+  chapter = 	 {Dilute Solutions},
+  pages   =      {89},
+  publisher = 	 {Oxford},
+  year = 	 {1952},
+}
+
+
+@book{hill1986statthermo,
+  title={An introduction to statistical thermodynamics},
+  author={Hill, Terrell L},
+  year={1986},
+  publisher={Dover Publications}
+}
+
+@Book{levine2009physicalchemistrybook6ed,
+  author = 	 {Levine, I. N.},
+  ALTeditor = 	 {},
+  title = 	 {Physical Chemistry},
+  publisher = 	 {McGraw-Hill},
+  year = 	 {2009},
+  edition = 	 {6th},
+}
+
+
+@article{mobley2014freesolv,
+  title={FreeSolv: a database of experimental and calculated hydration free energies, with input files},
+  author={Mobley, David L and Guthrie, J Peter},
+  journal={J. Comput. Aided Mol. Des.},
+  volume={28},
+  pages={711--720},
+  year={2014},
+  publisher={Springer},
+  doi = {10.1007/s10822-014-9747-x}
+}
+
+@article{nicholls2008predicting,
+  title={Predicting small-molecule solvation free energies: an informal blind test for computational chemistry},
+  author={Nicholls, Anthony and Mobley, David L and Guthrie, J Peter and Chodera, John D and Bayly, Christopher I and Cooper, Matthew D and Pande, Vijay S},
+  journal={J. Med. Chem.},
+  volume={51},
+  number={4},
+  pages={769--779},
+  year={2008},
+  doi = {10.1021/jm070549+},
+  publisher={ACS Publications}
+}
+
+@article{simonson2016physical,
+  title={The physical basis of ligand binding},
+  author={Simonson, Thomas},
+  journal={In Silico Drug Discovery and Design},
+  pages={3--43},
+  year={2016},
+  publisher={CRC Press}
+}
+
+@article{gallicchio2011recentadv,
+  title={Recent theoretical and computational advances for modeling protein--ligand binding affinities},
+  author={Gallicchio, Emilio and Levy, Ronald M},
+  journal={Adv. Prot. Chem. Struct. Biol.},
+  volume={85},
+  pages={27--80},
+  year={2011},
+  publisher={Elsevier},
+  doi = {10.1016/B978-0-12-386485-7.00002-8}
+}
+
+@InBook{gallicchio2021comppeptsci,
+  author = 	 {Emilio Gallicchio},
+  editor = 	 {Thomas Simonson},
+  title = 	 {Methods in Molecular Biology, Computational Peptide Science: Methods and Protocols},
+  chapter = 	 {Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria},
+  publisher = 	 {Springer Nature},
+  year = 	 {2021},
+  pages = 	 {303-334},
+  doi = {10.1007/978-1-0716-1855-4_15}
+}
+
+@Article{mihailescu2004theory,
+  Title                    = {On the theory of noncovalent binding.},
+  Author                   = {Mihail Mihailescu and Michael K Gilson},
+  Journal                  = {Biophys. J.},
+  Year                     = {2004},
+  Pages                    = {23--36},
+  Volume                   = {87},
+  doi                     = {10.1529/biophysj.103.031682}
+}
+
+@article{bennaim1984solvation,
+  title={Solvation thermodynamics of nonionic solutes},
+  author={Ben-Naim, A and Marcus, Y},
+  journal={J. Chem. Phys.},
+  volume={81},
+  number={4},
+  pages={2016--2027},
+  year={1984},
+  publisher={AIP Publishing}
+}
+
+@Article{rouxandsimonson1999solventmodels,
+  Title                    = {Implicit Solvent Models},
+  Author                   = {Roux, B. and Simonson, T.},
+  Journal                  = {Biophys. Chem.},
+  Year                     = {1999},
+  Pages                    = {1-20},
+  Volume                   = {78},
+  doi = {10.1016/S0301-4622(98)00226-9}
+}
+
+@Article{hermans1986freeenergy,
+  Title                    = {The free energy of xenon binding to myoglobin from molecular dynamics simulation},
+  Author                   = {Jan Hermans and Shankar Subramaniam},
+  Journal                  = {Isr. J. Chem.},
+  Year                     = {1986},
+  Pages                    = {225-227},
+  Volume                   = {27},
+  doi = {10.1002/ijch.198600032}
 }