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References

  • 1
    Li Z, Lazaridis T ( 2007) Water at biomolecular binding interfaces. Phys Chem Chem Phys 9: 573581.
  • 2
    Steinbach PJ, Brooks BR ( 1993) Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci USA 90: 91359139.
  • 3
    Loris R, Langhorst U, Vos SD, Decanniere K, Bouckaert J, Maes D, Transue TR, Steyaert J ( 1999) Conserved water molecules in a large family of microbial ribonucleases. Proteins: Struct Funct Genet 36: 117134.
  • 4
    Scheidig AJ, Burmester C, Goody RS ( 1999) The pre-hydrolysis state of p21ras in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. Structure 7: 13111324.
  • 5
    Tarek M, Tobias DJ ( 1999) Environmental dependence of the dynamics of protein hydration water. J Am Chem Soc 121: 97409741.
  • 6
    Ben-Naim A ( 2002) Molecular recognition–viewed through the eyes of the solvent. Biophys Chem 101102: 309–319.
  • 7
    Cheung MS, Garcia AE, Onuchic JN ( 2002) Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci USA 99: 685690.
  • 8
    Dunn RV, Daniel RM ( 2004) The use of gas-phase substrates to study enzyme catalysis at low hydration. Philos Trans R Soc Lond B 359: 13091320.
  • 9
    Halle B ( 2004) Protein hydration dynamics in solution: a critical survey. Philos Trans R Soc Lond B 359: 12071224.
  • 10
    Smolin N, Oleinikova A, Brovchenko I, Geiger A, Winter R ( 2005) Properties of spanning water networks at protein surfaces. J Phys Chem B 109: 1099511005.
  • 11
    Chaplin M ( 2006) Do we underestimate the importance of water in cell biology? Nature Rev Mol Cell Biol 7: 861866.
  • 12
    Scheiner S, Kar T, Pattanayak J ( 2002) Comparison of various types of hydrogen bonds involving aromatic amino acids. J Am Chem Soc 124: 1325713264.
  • 13
    Steiner T ( 2002) Hydrogen bonds from water molecules to aromatic acceptors in very high-resolution protein crystal structures. Biophys Chem 95: 195201.
  • 14
    Gallivan JP, Dougherty DA ( 1999) Can lone pairs bind to a π system? The water hexafluorobenzene interaction. Org Lett 1: 103106.
  • 15
    Sarkhel S, Rich A, Egli M ( 2003) Water-nucleobase “stacking”: H-π and lone pair-π interactions in the atomic resolution crystal structure of an RNA pseudoknot. J Am Chem Soc 125: 89988999.
  • 16
    Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF ( 2004) Unconventional interactions between water and heterocyclic nitrogens in protein structures. Proteins: Struct Funct Bioinf 57: 18.
  • 17
    Egli M, Sarkhel S ( 2007) Lone pair-aromatic interactions: To stabilize or not to stabilize. Acc Chem Res 40: 197205.
  • 18
    Mooibroek TJ, Gamez P, Reedijk J ( 2008) Lone pair-π interactions: a new supramolecular bond? Cryst Eng Comm 10: 15011515.
  • 19
    Schneider H-J, Werner F, Blatter T ( 1993) Attractive interactions between negative charges and polarizable aryl parts of host-guest systems. J Phys Org Chem 6: 590594.
  • 20
    Alkorta I, Rozas I, Elguero J ( 1997) An attractive interaction between the π-cloud of C6F6 and electron-donor atoms. J Org Chem 62: 46874691.
  • 21
    Danten Y, Tassaing T, Besnard M ( 1999) On the nature of the water-hexafluorobenzene interaction. J Phys Chem A 103: 35303534.
  • 22
    Mascal M, Armstrong A, Bartberger MD ( 2002) Anion-aromatic bonding: a case for anion recognition by π-acidic rings. J Am Chem Soc 124: 62746276.
  • 23
    Quiñonero D, Garau C, Rotger C, Frontera A, Ballester P, Costa A, Deyà PM ( 2002) Anion-π interactions: do they exist? Angew Chem Int Ed 41: 33893392.
  • 24
    Raimondi M, Calderoni G, Famulari A, Raimondi L, Cozzi F ( 2003) The benzene/water/hexafluorobenzene complex: a computational study. J Phys Chem A 107: 772774.
  • 25
    Jain A, Purohit CS, Verma S, Sankararamakrishnan R ( 2007) Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: π.π or lone-pair.π interactions? J Phys Chem B 111: 86808683.
  • 26
    Quinonero D, Frontera A, Escudero D, Ballester P, Costa A, Deya PM ( 2007) A theoretical study of anion-π interactions in seven-membered rings. Chemphyschem 8: 11821187.
  • 27
    Ringer AL, Senenko A, Sherrill CD ( 2007) Models of S/π interactions in protein structures: comparison of the H2S benzene complex with PDB data. Protein Sci 16: 22162223.
  • 28
    Gung BW, Zou Y, Xu Z, Amicangelo JC, Irwin DG, Ma S, Zhou HC ( 2008) Quantitative study of interactions between oxygen lone pair and aromatic rings: substituent effect and the importance of closeness of contact. J Org Chem 73: 689693.
  • 29
    Imai YN, Inoue Y, Nakanishi I, Kitaura K ( 2008) Cl-π interactions in protein-ligand complexes. Protein Sci 17: 11291137.
  • 30
    Reyes A, Fomina L, Rumsh L, Fomine S ( 2005) Are water-aromatic complexes always stabilized due to π-H interactions? LMP2 study. Int J Quantum Chem 104: 335341.
  • 31
    DiLabio GA, Johnson ER ( 2007) Lone pair-π and π.π interactions play an important role in proton-coupled electron transfer reactions. J Am Chem Soc 129: 61996203.
  • 32
    Parthasarathy S, Murthy MRN ( 2000) Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng 13: 913.
  • 33
    van Gunsteren WF, Billeter SR, Eising AA, Hunenberger PH, Kruger P, Mark AE, Scott WRP, Tironi IG ( 1996) Biomolecular simulation: the GROMOS96 manual and user guide. Vdf Hochschulverlag AG an der ETH. Zurich, Switzerland. pp 11042.
  • 34
    Daura X, Mark AE, van Gunsteren WF ( 1998) Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 19: 535547.
  • 35
    Weiss MS, Brandl M, Sühnel J, Pal D, Hilgenfeld R ( 2001) More hydrogen bonds for the (structural) biologist. Trends Biochem Sci 26: 521523.
  • 36
    Feller D ( 1999) Strength of the benzene-water hydrogen bond. J Phys Chem A 103: 75587561.
  • 37
    Mishra BK, Sathyamurthy N ( 2007) Van der waals complexes of small molecules with benzenoid rings: influence of multipole moments on their mutual orientation. J Phys Chem A 111: 21392147.
  • 38
    Garau C, Frontera A, Quinonero D, Ballester P, Costa A, Deya PM ( 2004) Cation-π versus anion-π interactions: energetic, charge transfer, and aromatic aspects. J Phys Chem A 108: 94239427.
  • 39
    Kim D, Tarakeshwar P, Kim KS ( 2004) Theoretical investigations of anion-π interactions: the role of anions and the nature of π systems. J Phys Chem A 108: 12501258.
  • 40
    Lovell SC, Davis IW, ArendallIIIWB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC ( 2003) Structure validation by Cα geometry: ϕ, φ and Cβ deviation. Proteins: Struct Funct Genet 50: 437450.
  • 41
    McDonald IK, Thornton JM ( 1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238: 777793.
  • 42
    Baker EN, Hubbard RE ( 1984) Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44: 97179.
  • 43
    Forrest LR, Honig B ( 2005) An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins: Struct Funct Bioinf 61: 296309.
  • 44
    Lindahl E, Hess B, van der Spoel D ( 2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306317.
  • 45
    Jorgensen WL, Maxwell DS, Tirado-Rives J ( 1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 1122511236.
  • 46
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JR, Vreven T, Kudin KN, Burant JC, Millam JM, lyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, lshida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA ( 2003) Gaussian 03, revision B.05; Gaussian, Inc., Pittsburgh PA.
  • 47
    Boys SF, Bernardi F ( 1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19: 553566.