Chapter 6 Citations

  1. Tanaka, K.; Mackay, G. I.; Payzant, J. D.; Bohme, D. K., "Gas-phase Reactions of Anions with Halogenated Methanes at 297 � 2 K," Can. J. Chem., 1976, 54, 1643-1659, DOI: 10.1139/v76-234.
  2. Olmstead, W. N.; Brauman, J. I., "Gas-Phase Nucleophilic Displacement Reactions," J. Am. Chem. Soc., 1977, 99, 4219-4228, DOI: 10.1021/ja00455a002.
  3. Pellerite, M. J.; Brauman, J. I., "Intrinsic Barriers in Nucleophilic Displacements. A General Model for Intrinsic Nucleophilicity Toward Methyl Centers," J. Am. Chem. Soc., 1983, 105, 2672-2680, DOI: 10.1021/ja00347a026.
  4. Beak, P., "Energies and Alkylations of Tautomeric Heterocyclic Compounds: Old Problems - New Answers," Acc. Chem. Res., 1977, 10, 186-192, DOI: 10.1021/ar50113a006.
  5. Brauman, J. I.; Blair, L. K., "Gas-Phase Acidities of Alcohols. Effects of Alkyl Groups.," J. Am. Chem. Soc., 1968, 90, 6561-6562, DOI: 10.1021/ja01025a083.
  6. Brauman, J. I.; Blair, L. K., "Gas-Phase Acidities of Alcohols," J. Am. Chem. Soc., 1970, 92, 5986-5992, DOI: 10.1021/ja00723a029.
  7. Cramer, C. J. Essential of Computational Chemistry: Theories and Models; John Wiley & Sons: New York, 2002.
  8. Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons: Chichester, England, 1999.
  9. Tomasi, J.; Persico, M., "Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent," Chem. Rev., 1994, 94, 2027-2094, DOI: 10.1021/cr00031a013.
  10. Cramer, C. J.; Truhlar, D. G., "Continuum Solvation Models: Classical and Quantum Mechanical Implementations," Rev. Comput. Chem., 1995, 6, 1-72.
  11. Cramer, C. J.; Truhlar, D. G., "Implicit Solvation Models: Equilbiria, Structure, Spectra, and Dynamics," Chem. Rev., 1999, 99, 2161-2200 , DOI: 10.1021/cr960149m.
  12. Bickelhaupt, F. M.; Baerends, E. J.; Nibbering, N. M. M., "The effect of microsolvation on E2 and SN2 reactions: theoretical study of the model system F- + C2H5F + nHF," Chemistry Eur. J., 1996, 2, 196-207.
  13. Okuno, Y., "Theoretical Examination of Solvent Reorganization and Nonequilibrium Solvation Effects in Microhydrated Reactions," J. Am. Chem. Soc., 2000, 122, 2925-2933, DOI: 10.1021/ja9940221.
  14. Raugei, S.; Cardini, G.; Schettino, V., "Microsolvation Effect on Chemical Reactivity: The Case of the Cl- + CH3Br SN2 Reaction," J. Chem. Phys., 2001, 114, 4089-4098, DOI: 10.1063/1.1348023.
  15. Re, S.; Morokuma, K., "ONIOM Study of Chemical Reaction in Microslvation Clusters: (H2O)nCH3Cl + OH-(H2O)m (n+m=1 and 2)," J. Phys. Chem. A, 2001, 105, 7185-7197, DOI: 10.1021/jp004623a.
  16. Takashima, K.; Riveros, J. M., "Gas-Phase Solvated Negative Ions," Mass Spectrom. Rev., 1998, 17, 409-430, DOI: 10.1002/(SICI)1098-2787(1998)17:6<409::AID-MAS2>3.0.CO;2-J.
  17. Laerdahl, J. K., "Gas Phase Nucleophilic Substitution," Int. J. Mass Spectrom., 2002, 214, 277-314, DOI: 10.1016/S1387-3806(01)00575-9.
  18. Roux, B.; Simonson, T., "Implicit Solvent Models," Biophys>. Chem., 1999, 78, 1-20, DOI: 10.1016/S0301-4622(98)00226-9.
  19. Miertus, S.; Scrocco, E.; Tomasi, J., "Electrostatic Interaction of a Solute with a Continuum. A Direct Utilization of ab Initio Molecular Potentials for the Prevision of Solvent Effects," Chem. Phys., 1981, 55, 117-129, DOI: 10.1016/0301-0104(81)85090-2.
  20. Cossi, M.; Barone, V.; Cammi, R.; Tomasi, J., "Ab Initio Study of Solvated Molecules: a New Implementation of the Polarizable Continuum Model," Chem. Phys. Lett., 1996, 255, 327-335, DOI: 10.1016/0009-2614(96)00349-1.
  21. Thompson, J. D.; Cramer, C. J.; Truhlar, D. G., "Parameterization of Charge Model 3 for AM1, PM3, BLYP, and B3LYP," J. Comput. Chem., 2003, 24, 1291-1304, DOI: 10.1002/jcc.10244.
  22. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G., "SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters," J. Chem. Theory Comput. 2005, 1, 1133-1152, DOI: 10.1021/ct050164b.
  23. Li, J.; Zhu, T.; Hawkins, G. D.; Winget, P.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G., "Extension of the Platform of Applicability of the SM5.42R Universal Solvation Model," Theor. Chem. Acc., 1999, 103, 9-63, DOI: 10.1007/s002140050513.
  24. Cramer, C. J.; Truhlar, D. G. In Solvent Effects and Chemical Reactivity; Tapia, O., Bertran, J., Eds.; Kluwer: Dordrecht, 1996, p 1-80.
  25. Canc�, E.; Mennucci, B.; Tomasi, J., "A New Integral Equation Formalism for the Polarizable Continuum Model: Theoretical Background and Applications to Isotropic and Anisotropic Dielectrics," J. Chem. Phys., 1997, 107, 3032-3041, DOI: 10.1063/1.474659.
  26. Barone, V.; Cossi, M.; Tomasi, J., "Geometry Optimization of Molecular Structures in Solution by the Polarizable Continuum Model," J. Comput. Chem., , 19, 404-417, DOI: 10.1002/(SICI)1096-987X(199803)19:4<404::AID-JCC3>3.0.CO;2-W.
  27. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V., "Polarizable Dielectric Model of Solvation with Inclusion of Charge Penetration Effects," J. Chem. Phys., 2001, 115, 5691-5701, DOI: 10.1063/1.1354187.
  28. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V., "New Developments in the Polarizable Continuum Model for Quantum Mechanical and Classical Calculations on Molecules in Solution," J. Chem. Phys., 2002, 117, 43-54, DOI: 10.1063/1.1480445.
  29. Orozco, M.; Luque, F. J., "Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems," Chem. Rev., 2000, 100, 4187-4226, DOI: 10.1021/cr990052a.
  30. Curutchet, C.; Orozco, M.; Luque, J. F., "Solvation in Octanol: Parametrization of the Continuum MST Model," J. Comput. Chem., 2001, 22, 1180-1193, DOI: 10.1002/jcc.1076.
  31. Foresman, J. B.; Keith, T. A.; Wiberg, K. B.; Snoonian, J.; Frisch, M. J., "Solvent Effects. 5. Influence of Cavity Shape, Truncation of Electrostatics, and Electron Correlation on ab Initio Reaction Field Calculations," J. Phys. Chem., 1996, 100, 16098-16104, DOI: 10.1021/jp960488j.
  32. Cramer, C. J.; Truhlar, D. G., "General Parameterized SCF Model for Free Energies of Solvation in Aqueous Solution," J. Am. Chem. Soc., 1991, 113, 8305-8311, DOI: 10.1021/ja00022a017.
  33. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G., "Universal Quantum Mechanical Model for Solvation Free Energies Based on Gas-Phase Geometries," J. Phys. Chem. B, 1998, 102, 3257-3271, DOI: 10.1021/jp973306+.
  34. Klamt, A.; Sch��rmann, G., "COSMO: a New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and its Gradient," J. Chem. Soc., Perkin Trans. 2, 1993, 799-805, DOI: 10.1039/P29930000799.
  35. Klamt, A.; Jonas, V.; Burger, T.; Lohrenz, J. C. W., "Refinement and Parametrization of COSMO-RS," J. Phys. Chem. A, 1998, 102, 5074-5085, DOI: 10.1021/jp980017s.
  36. Barone, V.; Cossi, M., "Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model," J. Phys. Chem. A, 1998, 102, 1995-2001, DOI: 10.1021/jp9716997.
  37. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V., "Energies, Structures, and Electronic Properties of Molecules in Solution with the C-PCM Solvation Model," J. Comput. Chem., 2003, 24, 669-681, DOI: 10.1002/jcc.10189.
  38. Curutchet, C.; Cramer, C. J.; Truhlar, D. G.; Ruiz-L�pez, M. F.; Rinaldi, D.; Orozco, M.; Luque, F. J., "Electrostatic Component of Solvation: Comparison of SCRF Continuum Models," J. Comput. Chem. 2003, 24, 284-297, DOI: 10.1002/jcc.10143.
  39. Adamo, C.; Barone, V., "Exchange Functionals with Improved Long-Range Behavior and Adiabatic Connection Methods without Adjustable Parameters: The mPW and mPW1PW Models," J. Chem. Phys., 1998, 108, 664-675, DOI: 10.1063/1.475428.
  40. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G., "Adding Explicit Solvent Molecules to Continuum Solvent Calculations for the Calculation of Aqueous Acid Dissociation Constants," J. Phys. Chem. A, 2006, 110, 2493-2499, DOI: 10.1021/jp055336f.
  41. Sauer, J.; Sustmann, R., "Mechanistic Aspects of Diels-Alder Reactions: A Critical Survey," Angew>. Chem. Int. Ed. Engl., 1980, 19, 779-807, DOI: 10.1002/anie.198007791.
  42. Dewar, M. J. S.; Pyron, R. S., "Nature of the Transition State in Some Diels-Alder Reactions," J. Am. Chem. Soc., 1970, 92, 3098-3103, DOI: 10.1021/ja00713a030.
  43. Beltrame, P., "Addition of Unsaturated Compounds to Each Other," Compr. Chem. Kinet., 1973, 9, 87-162.
  44. Rideout, D. C.; Breslow, R., "Hydrophobic Acceleration of Diels-Alder Reactions," J. Am. Chem. Soc., 1980, 102, 7816-7817, DOI: 10.1021/ja00546a048.
  45. Engberts, J. B. F. N., "Diels-Alder Reactions in Water: Enforced Hydrophobic Interaction and Hydrogen Bonding," Pure Appl. Chem., 1995, 67, 823-828,
  46. Breslow, R.; Maitra, U.; Rideout, D., "Selective Diels-Alder Reactions in Aqueous Solutions and Suspensions," Tetrahedron Lett., 1983, 24, 1901-1904, DOI: 10.1016/S0040-4039(00)81801-8.
  47. Breslow, R., "Hydrophobic Effects on Simple Organic Reactions in Water," Acc. Chem. Res., 1991, 24, 159-164, DOI: 10.1021/ar00006a001.
  48. Grieco, P. A.; Garner, P.; He, Z.-M., ""Micellar" Catalysis in the Aqueous Intermolecular Diels-Alder Reaction: Rate Acceleration and Enhanced Selectivity," Tetrahedron Lett., 1983, 24, 1897-1900, DOI: 10.1016/S0040-4039(00)81800-6.
  49. Grieco, P. A.; Nunes, J. J.; Gaul, M. D., "Dramatic Rate Accelerations of Diels-Alder Reactions in 5 M Lithium Perchlorate-Diethyl Ether: the Cantharidin Problem Reexamined," J. Am. Chem. Soc., 1990, 112, 4595-4596, DOI: 10.1021/ja00167a096.
  50. Schneider, H.-J.; Sangwan, N. K., "Diels�Alder Reactions in Hydrophobic Cavities: a Quantitative Correlation with Solvophobicity and Rate Enhancements by Macrocycles," J. Chem. Soc., Chem. Commun. 1986, 1787-1789, DOI: 10.1039/C39860001787.
  51. Schneider, H.-J.; Sangwan, N. K., "Changes of Stereoselectivity in Diels-Alder Reactions by Hydrophobic Solvent Effects and by style='font-family:Symbol'>b-Cyclodextrin," Angew. Chem. Int. Ed. Engl., 1987, 26, 896-897, DOI: 10.1002/anie.198708961.
  52. Blake, J. F.; Jorgensen, W. L., "Solvent Effects on a Diels-Alder Reaction from Computer Simulations," J. Am. Chem. Soc., 1991, 113, 7430-7432, DOI: 10.1021/ja00019a055.
  53. Birney, D. M.; Houk, K. N., "Transition Structures of the Lewis Acid-Catalyzed Diels-Alder Reaction of Butadiene with Acrolein. The Origins of Selectivity," J. Am. Chem. Soc., 1990, 112, 4127-4133, DOI: 10.1021/ja00167a005.
  54. Blake, J. F.; Lim, D.; Jorgensen, W. L., "Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States. Ab Initio Evidence," J. Org. Chem., , 59, 803-805, DOI: h10.1021/jo00083a021.
  55. Furlani, T. R.; Gao, J., "Hydrophobic and Hydrogen-Bonding Effects on the Rate of Diels-Alder Reactions in Aqueous Solution," J. Org. Chem., 1996, 61, 5492-5497, DOI: 10.1021/jo9518011.
  56. Chandrasekhar, J.; Shariffskul, S.; Jorgensen, W. L., "QM/MM Simulations for Diels-Alder Reactions in Water: Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effect," J. Phys. Chem. B, 2002, 106, 8078-8085, DOI: 10.1021/jp020326p.
  57. Kong, S.; Evanseck, J. D., "Density Functional Theory Study of Aqueous-Phase Rate Acceleration and <i>Endo/Exo</i> Selectivity of the Butadiene and Acrolein Diels-Alder Reaction," J. Am. Chem. Soc., 2000, 122, 10418-10427 , DOI: \10.1021/ja0010249.
  58. Kistiakowsky, G. B.; Lacher, J. R., "The Kinetics of Some Gaseous Diels-Alder Reactions," J. Am. Chem. Soc., 1936, 58, 123-133, DOI: ja01292a040.
  59. El Khadem, H. S. Carbohydrate Chemistry: Monosaccharides and their Oligomers; Academic Press: San Diego, CA, 1988.
  60. Collins, P.; Ferrier, R. Monosaccharides : Their Chemistry and their Roles in Natural Products; J. Wiley & Sons: Chichester, UK, 1995.
  61. Pierson, G. O.; Runquist, O. A., "Conformational Analysis of Some 2-Alkoxytetrahydropyrans," J. Org. Chem., 1968, 33, 2572-2574, DOI: 10.1021/jo01270a110.
  62. Kirby, A. J. The Anomeric Effect and Related Stereoelectronic Effects at Oxygen; Springer-Verlag: Berlin, 1982.
  63. Hommel, E. L.; Merle, J. K.; Ma, G.; Hadad, C. M.; Allen, H. C., "Spectroscopic and Computational Studies of Aqueous Ethylene Glycol Solution Surfaces," J. Phys. Chem. B, 2005, 109, 811-818, DOI: 10.1021/jp046715w.
  64. Csonka, G. I.; Csizmadia, I. G., "Density Functional Conformational Analysis of 1,2-Ethanediol," Chem. Phys. Lett. 1995, 243, 419-428, DOI: 10.1016/0009-2614(95)00846-V.
  65. Cramer, C. J.; Truhlar, D. G., "Quantum Chemical Conformational Analysis of 1,2-Ethanediol: Correlation and Solvation Effects on the Tendency To Form Internal Hydrogen Bonds in the Gas Phase and in Aqueous Solution," J. Am. Chem. Soc., 1994, 116, 3892-3900, DOI: 10.1021/ja00088a027.
  66. Howard, D. L.; Jorgensen, P.; Kjaergaard, H. G., "Weak Intramolecular Interactions in Ethylene Glycol Identified by Vapor Phase OH-Stretching Overtone Spectroscopy," J. Am. Chem. Soc., 2005, 127, 17096-17103, DOI: 10.1021/ja055827d.
  67. Crittenden, D. L.; Thompson, K. C.; Jordan, M. J. T., "On the Extent of Intramolecular Hydrogen Bonding in Gas-Phase and Hydrated 1,2-Ethanediol," J. Phys. Chem. A, 2005, 109, 2971-2977 , DOI: 10.1021/jp045233h.
  68. Klein, R. A., "Ab initio Conformational Studies on Diols and Binary Diol-Water Systems using DFT Methods. Intramolecular Hydrogen Bonding and 1:1 Complex Formation with Water," J. Comput. Chem., 2002, 23, 585-599, DOI: 10.1002/jcc.10053.
  69. Mandado, M.; Gra�a, A. M.; Mosquera, R. A., "Do 1,2-Ethanediol and 1,2-Dihydroxybenzene Present Intramolecular Hydrogen Hond?," Phys. Chem. Chem. Phys., 2004, 4391-4396, DOI: 10.1039/b406266c.
  70. Caminati, W.; Corbelli, G., "Conformation of Ethylene Glycol from the Rotational Spectra of the Nontunneling O-Monodeuterated Species," J. Mol. Spectrosc., 1981, 90, 572-578, DOI: 10.1016/0022-2852(81)90146-6.
  71. Buckley, P. D.; Giguere, P. A., "Infrared Studies on Rotational Isomerism. I. Ethylene Glycol," Can. J. Chem., 1967, 45, 397-407, DOI: 10.1139/v67-070.
  72. Pachler, K. G. R.; Wessels, P. L., "Rotational Isomerism. X. A Nuclear Magnetic Resonance Study of 2-Fluoro-ethanol and Ethylene Glycol," J. Mol. Struct., 1970, 6, 471-478, DOI: 10.1016/0022-2860(70)90029-3.
  73. Chaudhari, A.; Lee, S.-L., "A Computational Study of Microsolvation Effect on Ethylene Glycol by Density Functional Method," J. Chem. Phys., 2004, 120, 7464-7469, DOI: 10.1063/1.1688754.
  74. Callam, C. S.; Singer, S. J.; Lowary, T. L.; Hadad, C. M., "Computational Analysis of the Potential Energy Surfaces of Glycerol in the Gas and Aqueous Phases: Effects of Level of Theory, Basis Set, and Solvation on Strongly Intramolecularly Hydrogen-Bonded Systems," J. Am. Chem. Soc., 2001, 123, 11743-11754, DOI: 10.1021/ja011785r.
  75. Sheppard, N.; Turner, J. J., "High-Resolution Nuclear Magnetic Resonance (NMR) Spectra of Hydrocarbon Groupings. II. Internal Rotation in Substituted Ethanes and Cyclic Ethers," Proc. Roy. Soc. (London), 1959, A252, 506-519, 10.1098/rspa.1959.0169.
  76. Gutowsky, H. S.; Belford, G. G.; McMahon, P. E., "NMR Studies of Conformational Equilibria in Substituted Ethanes," J. Chem. Phys., 1962, 36, 3353-3368, DOI: 10.1063/1.1732468.
  77. da Silva, C. O.; Mennucci, B.; Vreven, T., "Density Functional Study of the Optical Rotation of Glucose in Aqueous Solution," J. Org. Chem., 2004, 69, 8161-8164, DOI: 10.1021/jo049147p.
  78. Carey, F. A. Organic Chemistry; 5th ed.; McGraw-Hill: Boston, 2003.
  79. Solomons, T. W. G.; Fryhle, C. B. Organic Chemistry; 8th ed.; John Wiley & Sons: Hoboken, NJ, 2004.
  80. Appell, M.; Strati, G.; Willett, J. L.; Momany, F. A., "B3LYP/6-311++G** Study of &alhpa;- and β-D-Glucopyranose and 1,5-Anhydro-D-glucitol: 4C1 and 1C4 chairs, 3,OB and B3,O Boats, and Skew-Boat Conformations," Carbohydrate Res., 2004, 339, 537-551, DOI: 10.1016/j.carres.2003.10.014.
  81. Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; French, A. D.; Truhlar, D. G., "Relative Stability of Alternative Chair Forms and Hydroxymethyl Conformations of α-D-Glucopyranose," Carbohydrate Res., 1995, 276, 219-251, DOI: 10.1016/0008-6215(95)00175-S.
  82. Ma, B.; Schaefer, H. F.; Allinger, N. L., "Theoretical Studies of the Potential Energy Surfaces and Compositions of the D-Aldo- and D-Ketohexoses," J. Am. Chem. Soc., 1998, 120, 3411-3422, DOI: 10.1021/ja9713439.
  83. Lii, J.-H.; Ma, M.; Allinger, N. L., "Importance of Selecting Proper Basis Set in Quantum Mechanical Studies of Potential Energy Surfaces of Carbohydrates," J. Comput. Chem., 1999, 20, 1593-1603, DOI: 10.1002/(SICI)1096-987X(19991130)20:15<1593::AID-JCC1>3.0.CO;2-A.
  84. Hoffmann, M.; Rychlewski, J., "Effects of Substituting a OH Group by a F Atom in D-Glucose. Ab Initio and DFT Analysis," J. Am. Chem. Soc., 2001, 123, 2308-2316, DOI: 10.1021/ja003198w.
  85. Barrows, S. E.; Storer, J. W.; Cramer, C. J.; French, A. D.; Truhlar, D. G., "Factors Controlling Relative Stability of Anomers and Hydroxymethyl Conformers of Glucopyranose," J. Comput. Chem. 1998, 19, 1111-1129, DOI: 10.1002/(SICI)1096-987X(19980730)19:10<1111::AID-JCC1>3.0.CO;2-P.
  86. Momany, F. A.; Appell, M.; Strati, G.; Willett, J. L., "B3LYP/6-311++G** Study of Monohydrates of α- and β-D-Glucopyranose: Hydrogen Bonding, Stress Energies, and Effect of Hydration on Internal Coordinates," Carbohydrate Res., 2004, 339, 553-567, DOI: 10.1016/j.carres.2003.10.013.
  87. Wladkowski, B. D.; Chenoweth, S. A.; Jones, K. E.; Brown, J. W., "Exocyclic Hydroxymethyl Rotational Conformers of β- and α-D- Glucopyranose in the Gas Phase and Aqueous Solution," J. Phys. Chem. A, 1998, 102, 5086-5092, DOI: 10.1021/jp980524+.
  88. The Merck Index; 11th ed.; Budavari, S., Ed.; Merck & Co.: Rahway, New Jersey, 1989.
  89. Nishida, Y.; Ohrui, H.; Meguro, H., "1H-NMR Studies of (6R)- and (6S)-Deuterated D-Hexoses: Assignment of the Preferred Rotamers about C5---C6 Bond of D-Glucose and D-Galactose Derivatives in Solutions," Tetrahedron Lett., 1984, 25, 1575-1578, DOI: 10.1016/S0040-4039(01)90014-0.
  90. Rockwell, G. D.; Grindley, T. B., "Effect of Solvation on the Rotation of Hydroxymethyl Groups in Carbohydrates," J. Am. Chem. Soc., 1998, 120, 10953-10963, DOI: 10.1021/ja981958l.
  91. Poppe, L.; van Halbeek, H., "The Rigidity of Sucrose: Just an Illusion?," J. Am. Chem. Soc., 1992, 114, 1092-1094, DOI: 10.1021/ja00029a051.
  92. Adams, B.; Lerner, L., "Observation of Hydroxyl Protons of Sucrose in Aqueous Solution: No Evidence for Persistent Intramolecular Hydrogen Bonds," J. Am. Chem. Soc., 1992, 114, 4827-4829, DOI: 10.1021/ja00038a055.
  93. Engelsen, S. B.; du Penhoat, C. H.; Perez, S., "Molecular Relaxation of Sucrose in Aqueous Solutions: How a Nanosecond Molecular Dynamics Simulation Helps to Reconcile NMR Data," J. Phys. Chem., 1995, 99, 13334-13351, DOI: 10.1021/j100036a005.
  94. Batta, G.; K�v�r, K. E., "Heteronuclear coupling constants of hydroxyl protons in a water solution of oligosaccharides: trehalose and sucrose," Carbohydrate Res., 1999, 320, 267-272, DOI: 10.1016/S0008-6215(99)00183-4.
  95. Venable, R. M.; Delaglio, F.; Norris, S. E.; Freedberg, D. I., "The Utility of Residual Dipolar Couplings in Detecting Motion in Carbohydrates: Application to Sucrose," Carbohydrate Res., 2005, 340, 863-874, DOI: 10.1016/j.carres.2005.01.025.
  96. Momany, F. A.; Appell, M.; Willett, J. L.; Bosma, W. B., "B3LYP/6-311++G** Geometry-Optimization Study of Pentahydrates of sα- and β-D- glucopyranose," Carbohydrate Res., 2005, 340, 1638-1655, DOI: 10.1016/j.carres.2005.04.020.
  97. Watson, J. D.; Crick, F. H. C., "A Structure for Deoxyribose Nucleic Acid," Nature, 1953, 171, 737-738, DOI: 10.1038/171737a0.
  98. Judson, H. F. The Eighth Day of Creation: Makers of the Revolution in Biology; Cold Spring Harbor Press: Plainview, N.Y, 1996.
  99. Topal, M. D.; Fresco, J. R., "Complementary Base Pairing and the Origin of Substitution Mutations," Nature, 1976, 263, 285-289,
  100. Morgan, A. R., "Base Mismatches and Mutagenesis: How Important is Tautomerism ?," Trends Biochem. Sci., 1993, 18, 160-163, DOI: 10.1016/0968-0004(93)90104-U.
  101. Vonborstel, R. C., "Origins of Spontaneous Base Substitutions," Mutation Res., 1994, 307, 131-140, DOI: 10.1016/0027-5107(94)90285-2.
  102. Harris, V. H.; Smith, C. L.; Cummins, W. J.; Hamilton, A. L.; Adams, H.; Dickman, M.; Hornby, D. P.; Williams, D. M., "The Effect of Tautomeric Constant on the Specificity of Nucleotide Incorporation during DNA Replication: Support for the Rare Tautomer Hypothesis of Substitution Mutagenesis," J. Mol. Biol., 2003, 326, 1389-1401, DOI: 10.1016/S0022-2836(03)00051-2.
  103. Zhanpeisov, N. U.; Sponer, J.; Leszczynski, J., "Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine Base Pairs Stabilized by the Formation of the Minor Tautomers of Bases. An ab Initio Study in the Gas Phase and in a Water Cluster," J. Phys. Chem. A, 1998, 102, 10374-10379, DOI: 10.1021/jp9827126.
  104. Barsky, D.; Colvin, M. E., "Guanine-Cytosine Base Pairs in Parallel-Stranded DNA: An ab Initio Study of the Keto-Amino Wobble Pair versus the Enol-Imino Minor Tautomer Pair," J. Phys. Chem. A, 2000, 104, 8570-8576, DOI: 10.1021/jp001420d.
  105. Trygubenko, S. A.; Bogdan, T. V.; Rueda, M.; Orozco, M.; Luque, F. J.; Sponer, J.; Slav�ek, P.; Hobza, P.,"Correlated ab initio, Study of Nucleic Acid Bases and their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Part 1. Cytosine," Phys. Chem. Chem. Phys., 2002, 4192-4203, DOI: 10.1039/b202156k.
  106. Sambrano, J. R.; de Souza, A. R.; Queralt, J. J.; Andr�s, J., "A Theoretical Study on Cytosine Tautomers in Aqueous Media by using Continuum Models," Chem. Phys. Lett., 2000, 317, 437-443, DOI: 10.1016/S0009-2614(99)01394-9.
  107. Feyereisen, M.; Fitzgerald, G.; Komornicki, A., "Use of Approximate Integrals in ab Initio Theory. An Application in MP2 Energy Calculations," Chem. Phys. Lett. 1993, 208, 359-363, DOI: 10.1016/0009-2614(93)87156-W.
  108. Alem�n, C., "Solvation of Cytosine and Thymine Using a Combined Discrete/SCRF Model," Chem. Phys. Lett., 1999, 302, 461-470, DOI: 10.1016/S0009-2614(99)00173-6.
  109. Hunter, K. C.; Rutledge, L. R.; Wetmore, S. D., "The Hydrogen Bonding Properties of Cytosine: A Computational Study of Cytosine Complexed with Hydrogen Fluoride, Water, and Ammonia," J. Phys. Chem. A, 2005, 109, 9554-9562, DOI: 10.1021/jp0527709.
  110. Shishkin, O. V.; Gorb, L.; Leszczynski, J., "Does the Hydrated Cytosine Molecule Retain the Canonical Structure? A DFT Study," J. Phys. Chem. B, 2000, 104, 5357-5361, DOI: 10.1021/jp993144c.
  111. Hanus, M.; Ryjacek, F.; Kabelac, M.; Kubar, T.; Bogdan, T. V.; Trygubenko, S. A.; Hobza, P., "Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous Solution," J. Am. Chem. Soc., 2003, 125, 7678-7688, DOI: 10.1021/ja034245y.
  112. Jang, Y. H.; Goddard, W. A.; Noyes, K. T.; Sowers, L. C.; Hwang, S.; Chung, D. S., " pKa Values of Guanine in Water: Density Functional Theory Calculations Combined with Poisson-Boltzmann Continuum-Solvation Model," J. Phys. Chem. B, 2003, 107, 344-357, DOI: 10.1021/jp020774x.
  113. Colominas, C.; Luque, F. J.; Orozco, M., "Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded Complexes," J. Am. Chem. Soc., 1996, 118, 6811-6821, DOI: 10.1021/ja954293l.
  114. Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M., "Tautomerism of the DNA Base Guanine and Its Methylated Derivatives as Studied by Gas-Phase Infrared and Ultraviolet Spectroscopy," J. Phys. Chem. A, 2002, 106, 5088-5094, DOI: 10.1021/jp0139742.
  115. Hanus, M.; Kabelac, M.; Rejnek, J.; Ryjacek, F.; Hobza, P., "Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment, and in Aqueous Solution. Part 3. Adenine," J. Phys. Chem. B, 2004, 108, 2087-2097, DOI: 10.1021/jp036090m.
  116. Sukhanov, O. S.; Shishkin, O. V.; Gorb, L.; Podolyan, Y.; Leszczynski, J., "Molecular Structure and Hydrogen Bonding in Polyhydrated Complexes of Adenine: A DFT Study," J. Phys. Chem. B, 2003, 107, 2846-2852, DOI: 10.1021/jp026487a.
  117. Laxer, A.; Major, D. T.; Gottlieb, H. E.; Fischer, B., "(15N5)-Labeled Adenine Derivatives: Synthesis and Studies of Tautomerism by 15N NMR Spectroscopy and Theoretical Calculations," J. Org. Chem., 2001, 66, 5463-5481, DOI: 10.1021/jo010344n.
  118. Rejnek, J.; Hanus, M.; Kabel�, M.; Ryj�ek, F.; Hobza, P., "Correlated ab initio Study of Nucleic Acid Bases and their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Part 4. Uracil and Thymine," Phys. Chem. Chem. Phys., 2005, 2006-2017, DOI: 10.1039/b501499a.
  119. Kryachko, E. S.; Nguyen, M. T.; Zeegers-Huyskens, T., "Theoretical Study of Uracil Tautomers. 2. Interaction with Water," J. Phys. Chem.> A, 2001, 105, 1934-1943, DOI: 10.1021/jp0019411.
  120. Morsy, M. A.; Al-Somali, A. M.; Suwaiyan, A., "Fluorescence of Thymine Tautomers at Room Temperature in Aqueous Solutions," J. Phys. Chem. B, 1999, 103, 11205-11210, DOI: 10.1021/jp990858e.
  121. Hobza, P.; Sponer, J., "Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio, Calculations," Chem. Rev., 1999, 99, 3247-3276, DOI:
  122. Sponer, J.; Hobza, P., "Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies," Coll. Czech. Chem. Commun., 2003, 68, 2231-2282, DOI: 10.1135/cccc20032231.
  123. Sponer, J.; Jurecka, P.; Hobza, P., "Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs," J. Am. Chem. Soc., 2004, 126, 10142-10151, DOI: 10.1021/ja048436s.
  124. Zhao, Y.; Truhlar, D. G., "Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions," J. Phys. Chem. A, 2004, 108, 6908-6918, DOI: 10.1021/jp048147q.
  125. Zhao, Y.; Truhlar, D. G., "Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions," J. Phys. Chem. A, 2005, 109, 5656-5667, DOI: 10.1021/jp050536c.
  126. Zhanpeisov, N. U.; Leszczynski, J., "The Specific Solvation Effects on the Structures and Properties of Adenine-Uracil Complexes: A Theoretical ab Initio, Study," J. Phys. Chem. A, 1998, 102, 6167-6172, DOI: 10.1021/jp9806260.
  127. Zhao, Y.; Truhlar, D. G., "How well can new-generation density functional methods describe stacking interactions in biological systems ?," Phys. Chem. Chem. Phys., 2005, 7, 2701-2705, DOI: 10.1039/b507036h.
  128. Cerny, J.; Hobza, P., "The X3LYP Extended Density Functional Accurately Describes H-Bonding but Fails Completely for Stacking," Phys. Chem. Chem. Phys., 2005, 7, 1624 - 1626, DOI: 10.1039/b502769c.
  129. Sponer, J.; Leszczynski, J.; Hobza, P., "Nature of Nucleic Acid-Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs," J. Phys. Chem., 1996, 100, 5590-5596, DOI: 10.1021/jp953306e.
  130. Sponer, J.; Jurecka, P.; Marchan, I.; Luque, F. J.; Orozco, M.; Hobza, P., "Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps," Chem. Eur. J., 2006, 12, 2854-2865, DOI: 10.1002/chem.200501239.
  131. Jurecka, P.; Hobza, P., "True Stabilization Energies for the Optimal Planar Hydrogen-Bonded and Stacked Structures of Guanine...Cytosine, Adenine...Thymine, and Their 9- and 1-Methyl Derivatives: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels and Comparison with Experiment," J. Am. Chem. Soc., 2003, 125, 15608-15613, DOI: 10.1021/ja036611j.
  132. Hobza, P.; Sponer, J.; Reschel, T., "Density Functional Theory and Molecular Clusters," J. Comput. Chem., 1995, 16, 1315-1325, DOI: 10.1002/jcc.540161102.
  133. Zendlov�, L.; Hobza, P.; Kabel�c, M., "Potential Energy Surfaces of the Microhydrated Guanine...Cytosine Base Pair and its Methylated Analogue," ChemPhysChem, 2006, 7, 439-447, DOI: 10.1002/cphc.200500311.
  134. Kabelac, M.; Zendlova, L.; Reha, D.; Hobza, P., "Potential Energy Surfaces of an Adenine-Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules: Molecular Mechanics and Correlated Ab Initio Study," J. Phys. Chem. B, 2005, 109, 12206-12213, DOI: 10.1021/jp045970d.
  135. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A., "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules," J. Am. Chem. Soc., 1995, 117, 5179-5197, DOI: 10.1021/ja00124a002.
  136. Scuseria, G. E., "Linear Scaling Density Functional Calculations with Gaussian Orbitals," J. Phys. Chem. A, 1999, 103, 4782-4790, DOI: 10.1021/jp990629s.
  137. Chen, X. H.; Zhang, J. Z. H., "Theoretical Method for Full ab Initio Calculation of DNA/RNA�Ligand Interaction Energy," J. Chem. Phys., 2004, 120, 11386-11391, DOI: 10.1063/1.1737295.
  138. Miller, J. H.; Aceves-Gaona, A.; Ernst, M. B.; Haranczyk, M.; Gutowski, M.; Vorpagel, E. R.; Dupuis, M., "Structure and Energetics of Clustered Damage Sites," Radiation Res., 2005, 164, 582�585, DOI: 10.1667/RR3381.1.