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Chapter 7 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. Essentials 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. Tomasi, J.; Mennucci, B.; Cammi, R. "Quantum Mechanical Continuum Solvation Models," Chem. Rev. 2005, 10.1021/cr9904009.
  11. Cramer, C. J.; Truhlar, D. G. "Continuum Solvation Models: Classical and Quantum Mechanical Implementations," Rev. Comput. Chem. 1995, 6, 1-72, DOI: 10.1002/9780470125830.ch1.
  12. Cramer, C. J.; Truhlar, D. G. "Implicit Solvation Models: Equilbiria, Structure, Spectra, and Dynamics," Chem. Rev. 1999, 99, 2161-2200, DOI: 10.1021/cr960149m.
  13. Cramer, C. J.; Truhlar, D. G. "A Universal Approach to Solvation Modeling," Acc. Chem. Res. 2008, 41, 760-768, DOI: 10.1021/ar800019z.
  14. Mennucci, B. "Polarizable continuum model," WIREs Comput. Mol. Sci. 2012, 2, 386-404, DOI: 10.1002/wcms.1086.
  15. 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.
  16. 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.
  17. Beltrame, P. "Addition of Unsaturated Compounds to Each Other," Compr. Chem. Kinet. 1973, 9, 87-162.
  18. Rideout, D. C.; Breslow, R. "Hydrophobic Acceleration of Diels-Alder Reactions," J. Am. Chem. Soc. 1980, 102, 7816-7817, DOI: 10.1021/ja00546a048.
  19. Engberts, J. B. F. N. "Diels-Alder Reactions in Water: Enforced Hydrophobic Interaction and Hydrogen Bonding," Pure Appl. Chem. 1995, 67, 823-828, DOI: 10.1351/pac199567050823.
  20. 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.
  21. Breslow, R. "Hydrophobic Effects on Simple Organic Reactions in Water," Acc. Chem. Res. 1991, 24, 159-164, DOI: 10.1021/ar00006a001.
  22. 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.
  23. 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.
  24. 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.
  25. Schneider, H.-J.; Sangwan, N. K. "Changes of Stereoselectivity in Diels-Alder Reactions by Hydrophobic Solvent Effects and by β-Cyclodextrin," Angew. Chem. Int. Ed. Engl. 1987, 26, 896-897, DOI: 10.1002/anie.198708961.
  26. 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
  27. 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.
  28. Blake, J. F.; Lim, D.; Jorgensen, W. L. "Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States. Ab Initio Evidence," J. Org. Chem. 1994, 59, 803-805, DOI: 10.1021/jo00083a021.
  29. 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.
  30. 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.
  31. Acevedo, O.; Jorgensen, W. L. "Understanding Rate Accelerations for Diels−Alder Reactions in Solution Using Enhanced QM/MM Methodology," J. Chem. Theor. Comput. 2007, 3, 1412-1419, DOI: 10.1021/ct700078b.
  32. 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.
  33. Kistiakowsky, G. B.; Lacher, J. R. "The Kinetics of Some Gaseous Diels-Alder Reactions," J. Am. Chem. Soc. 1936, 58, 123-133, DOI: 10.1021/ja01292a040.
  34. El Khadem, H. S. Carbohydrate Chemistry: Monosaccharides and their Oligomers; Academic Press: San Diego, CA, 1988.
  35. Collins, P.; Ferrier, R. Monosaccharides: Their Chemistry and their Roles in Natural Products; J. Wiley & Sons: Chichester, UK, 1995.
  36. Pierson, G. O.; Runquist, O. A. "Conformational Analysis of Some 2-Alkoxytetrahydropyrans," J. Org. Chem. 1968, 33, 2572-2574, DOI: 10.1021/jo01270a110.
  37. Kirby, A. J. The Anomeric Effect and Related Stereoelectronic Effects at Oxygen; Springer-Verlag: Berlin, 1982.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. Mandado, M.; Graña, 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. Kumar, R. M.; Baskar, P.; Balamurugan, K.; Das, S.; Subramanian, V. "On the Perturbation of the H-Bonding Interaction in Ethylene Glycol Clusters upon Hydration," J. Phys. Chem. A 2012, 116, 4239-4247, DOI: 10.1021/jp300693r.
  50. 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.
  51. Jeong, K.-H.; Byun, B.-J.; Kang, Y.-K. "Conformational Preferences of Glycerol in the Gas Phase and in Water," Bull. Lorean Chem. Soc. 2012, 33, 917-924, DOI: 10.5012/bkcs.2012.33.3.917.
  52. 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, DOI: 10.1098/rspa.1959.0169.
  53. 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.
  54. 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.
  55. Carey, F. A. Organic Chemistry; 5th ed.; McGraw-Hill: Boston, 2003.
  56. Solomons, T. W. G.; Fryhle, C. B. Organic Chemistry; 10th ed.; John Wiley & Sons: Hoboken, NJ, 2011.
  57. Appell, M.; Strati, G.; Willett, J. L.; Momany, F. A. "B3LYP/6-311++G** Study of α- 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. Sameera, W. M. C.; Pantazis, D. A. "A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides," J. Chem. Theory Comput. 2012, 8, 2630-2645, DOI: 10.1021/ct3002305.
  63. 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.
  64. Momany, F. A.; Appell, M.; Strati, G.; Willett, J. L. "B3LYP/6-311++G** Study of Monohydrates of &alpha'- 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.
  65. 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+.
  66. The Merck Index; 11th ed.; Budavari, S., Ed.; Merck & Co.: Rahway, New Jersey, 1989.
  67. Mennucci, B.; Cappelli, C.; Cammi, R.; Tomasi, J. "Modeling solvent effects on chiroptical properties," Chirality 2011, 23, 717-729, DOI: 10.1002/chir.20984.
  68. 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.
  69. 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.
  70. Schnupf, U.; Willett, J. L.; Momany, F. "DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies," Carbohydrate Res. 2010, 345, 503-511, DOI: 10.1016/j.carres.2009.12.001.
  71. Poppe, L.; van Halbeek, H. "The Rigidity of Sucrose: Just an Illusion?," J. Am. Chem. Soc. 1992, 114, 1092-1094, DOI: 10.1021/ja00029a051.
  72. 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.
  73. 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.
  74. Batta, G.; Kövér, 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.
  75. 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.
  76. Momany, F. A.; Appell, M.; Willett, J. L.; Bosma, W. B. "B3LYP/6-311++G** Geometry-Optimization Study of Pentahydrates of α- and β-D-glucopyranose," Carbohydrate Res. 2005, 340, 1638-1655, DOI: 10.1016/j.carres.2005.04.020.
  77. Watson, J. D.; Crick, F. H. C. "A Structure for Deoxyribose Nucleic Acid," Nature 1953, 171, 737-738, DOI: 10.1038/171737a0.
  78. Judson, H. F. The Eighth Day of Creation: Makers of the Revolution in Biology; Cold Spring Harbor Press: Plainview, N.Y, 1996.
  79. Kabelac, M.; Hobza, P. "Hydration and stability of nucleic acid bases and base pairs," Phys. Chem. Chem. Phys. 2007, 9, 903-917, DOI: 10.1039/B614420A.
  80. Topal, M. D.; Fresco, J. R. "Complementary Base Pairing and the Origin of Substitution Mutations," Nature 1976, 263, 285-289, DOI: 10.1038/263285a0.
  81. 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.
  82. Vonborstel, R. C. "Origins of Spontaneous Base Substitutions," Mutation Res. 1994, 307, 131-140, DOI: 10.1016/0027-5107(94)90285-2.
  83. 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.
  84. 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.
  85. 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.
  86. Trygubenko, S. A.; Bogdan, T. V.; Rueda, M.; Orozco, M.; Luque, F. J.; Sponer, J.; Slavíek, 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.
  87. Sambrano, J. R.; de Souza, A. R.; Queralt, J. J.; Andrés, 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.
  88. Bazso, G.; Tarczay, G.; Fogarasi, G.; Szalay, P. G. "Tautomers of cytosine and their excited electronic states: a matrix isolation spectroscopic and quantum chemical study," Phys. Chem. Chem. Phys. 2011, 13, 6799-6807, DOI: 10.1039/C0CP02354J.
  89. Kosenkov, D.; Kholod, Y.; Gorb, L.; Shishkin, O.; Hovorun, D. M.; Mons, M.; Leszczynski, J. "Ab Initio Kinetic Simulation of Gas-Phase Experiments: Tautomerization of Cytosine and Guanine," J. Phys. Chem. B 2009, 113, 6140-6150, DOI: 10.1021/jp810570w.
  90. Alemán, 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.
  91. 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.
  92. 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.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. Kim, H.-S.; Ahn, D.-S.; Chung, S.-Y.; Kim, S. K.; Lee, S. "Tautomerization of Adenine Facilitated by Water:  Computational Study of Microsolvation," J. Phys. Chem. A 2007, 111, 8007-8012, DOI: 10.1021/jp074229d.
  98. 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.
  99. 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.
  100. 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.
  101. Rejnek, J.; Hanus, M.; Kabelá, M.; Ryjáek, 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.
  102. 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.
  103. 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.
  104. 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: 10.1021/cr9800255.
  105. 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.
  106. Sponer, J.; Riley, K. E.; Hobza, P. "Nature and magnitude of aromatic stacking of nucleic acid bases," Phys. Chem. Chem. Phys. 2008, 10, 2595-2610, DOI: 10.1039/B719370J.
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. 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.
  116. Hobza, P.; Sponer, J.; Reschel, T. "Density Functional Theory and Molecular Clusters," J. Comput. Chem. 1995, 16, 1315-1325, DOI: 10.1002/jcc.540161102.
  117. Morgado, C. A.; Jurečka, P.; Svozil, D.; Hobza, P.; Šponer, J. i. "Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description," J. Chem. Theor. Comput. 2009, 5, 1524-1544, DOI: 10.1021/ct9000125.
  118. Morgado, C. A.; Jurecka, P.; Svozil, D.; Hobza, P.; Sponer, J. "Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions," Phys. Chem. Chem. Phys. 2010, 12, 3522-3534, DOI: 10.1039/B924461A.
  119. Zendlova, L.; Hobza, P.; Kabelác, 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.
  120. 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.
  121. 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.
  122. Poater, J.; Swart, M.; Guerra, C. F.; Matthias Bickelhaupt, F. "Solvent effects on hydrogen bonds in Watson-Crick, mismatched, and modified DNA base pairs," Comput. Theor. Chem. 2012, 998, 57-63, DOI: 10.1016/j.comptc.2012.06.003.
  123. Poater, J.; Swart, M.; Guerra, C. F.; Bickelhaupt, F. M. "Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, π-stacking and solvent effects," Chem. Commun. 2011, 47, 7326-7328, DOI: 10.1039/C0CC04707D.
  124. Godfrey, P. D.; Brown, R. D. "Shape of Glycine," J. Am. Chem. Soc. 1995, 117, 2019-2023, DOI: 10.1021/ja00112a015.
  125. McGlone, S. J.; Elmes, P. S.; Brown, R. D.; Godfrey, P. D. "Molecular structure of a conformer of glycine by microwave spectroscopy," J. Mol. Struct. 1999, 485-486, 225-238, DOI: 10.1016/S0022-2860(99)00181-7.
  126. Ding, Y.; Krogh-Jespersen, K. "The glycine zwitterion does not exist in the gas phase: results from a detailed ab initio electronic structure study," Chem. Phys. Lett. 1992, 199, 261-266, DOI: 10.1016/0009-2614(92)80116-S.
  127. Kasalová, V.; Allen, W. D.; Schaefer III, H. F.; Czinki, E.; Császár, A. G. "Molecular Structures of the Two Most Stable Conformers of Free Glycine," J. Comput. Chem. 2007, 28, 1373-1383, DOI: 10.1002/jcc.20680.
  128. Alonso, J. L.; Cocinero, E. J.; Lesarri, A.; Sanz, M. E.; López, J. C. "The Glycine-Water Complex," Angew. Chem. Int. Ed. 2006, 45, 3471-3474, DOI: 10.1002/anie.200600342.
  129. Balabin, R. M. "The First Step in Glycine Solvation: The Glycine−Water Complex," J. Phys. Chem. B 2010, 114, 15075-15078, DOI: 10.1021/jp107539z.
  130. Jensen, J. H.; Gordon, M. S. "On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion," J. Am. Chem. Soc. 1995, 117, 8159-8170, DOI: 10.1021/ja00136a013.
  131. Aikens, C. M.; Gordon, M. S. "Incremental Solvation of Nonionized and Zwitterionic Glycine," J. Am. Chem. Soc. 2006, 128, 12835-12850, DOI: 10.1021/ja062842p.
  132. Wang, W.; Pu, X.; Zheng, W.; Wong, N.-B.; Tian, A. "Some Theoretical Observations on the 1:1 Glycine Zwitterion-Water Complex," J. Mol. Struct. (THEOCHEM) 2003, 626, 127-132, DOI: 10.1016/S0166-1280(03)00075-7.
  133. Bachrach, S. M. "Microsolvation of Glycine: A DFT Study," J. Phys. Chem. A 2008, 112, 3722-3730, DOI: 10.1021/jp711048c.
  134. Bachrach, S. M.; Nguyen, T. T.; Demoin, D. W. "Microsolvation of Cysteine: A Density Functional Theory Study," J. Phys. Chem. A 2009, 113, 6172-6181, DOI: 10.1021/jp901491p.
  135. Blom, M. N.; Compagnon, I.; Polfer, N. C.; vonHelden, G.; Meijer, G.; Suhai, S.; Paizs, B.; Oomens, J. "Stepwise Solvation of an Amino Acid: The Appearance of Zwitterionic Structures," J. Phys. Chem. A 2007, 111, 7309-7316, DOI: 10.1021/jp070211r.
  136. Mullin, J. M.; Gordon, M. S. "Alanine: Then There Was Water," J. Phys. Chem. B 2009, 113, 8657-8669, DOI: 10.1021/jp901459y.