Structural analysis of α-fetoprotein (AFP)-like peptides with anti-breast-cancer properties

Journal of Physical Chemistry B

Volumn 118, Issue 17, 2014, Pages 4514-4526

  Temelso, Berhane ^a,b   Alser, Katherine A ^a   Gauthier, Arianne ^b   Palmer, Amber Kay ^b   Shields, George C ^a,b  

^a BUCKNELL UNIVERSITY   (United States)

^b Armstrong State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASCORBIC ACID; DISEASES; PEPTIDES; QUANTUM CHEMISTRY;

COMPUTATIONAL STUDIES; DENSITY-FUNCTIONAL METHODS; ENERGY CONFORMERS; ESTROGEN RECEPTOR; OPTIMIZED STRUCTURES; PEPTIDE STRUCTURES; QUANTUM CHEMICAL CALCULATIONS; REPLICA EXCHANGE MOLECULAR DYNAMICS;

AMINO ACIDS;

ALPHA FETOPROTEIN; ANTINEOPLASTIC AGENT; PEPTIDE;

BREAST NEOPLASMS; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

ALPHA-FETOPROTEINS; ANTINEOPLASTIC AGENTS; BREAST NEOPLASMS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 84899814373     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp500017b     Document Type: Article

References (148)

1. Leclercq, G.; Gallo, D.; Cossy, J.; Laios, I.; Larsimont, D.; Laurent, G.; Jacquot, Y. Peptides Targeting Estrogen Receptor Alpha-Potential Applications for Breast Cancer Treatment Curr. Pharm. Des. 2011, 17, 2632-2653
2. Rosales-Hernandez, M. C.; Bermudez-Lugo, J.; Garcia, J.; Trujillo-Ferrara, J.; Correa-Basurto, J. Molecular Modeling Applied to Anti-Cancer Drug Development Anticancer Agents Med. Chem. 2009, 9, 230-238
3. Jacobson, H.; Bennett, J.; Mizejewski, G. Inhibition of Estrogen-Dependent Breast-Cancer Growth by a Reaction-Product of Alpha-Fetoprotein and Estradiol Cancer Res. 1990, 50, 415-420
4. Mizejewski, G. J.; Dias, J. A.; Hauer, C. R.; Henrikson, K. P.; Gierthy, J. Alpha-fetoprotein derived synthetic peptides: Assay of an estrogen-modifying regulatory segment Mol. Cell. Endocrinol. 1996, 118, 15-23
5. Eisele, L. E.; Mesfin, F. B.; Bennett, J. A.; Andersen, T. T.; Jacobson, H. I.; Soldwedel, H.; MacColl, R.; Mizejewski, G. J. Studies on a growth-inhibitory peptide derived from alpha-fetoprotein and some analogs J. Pept. Res. 2001, 57, 29-38
6. Mizejewski, G. J.; Butterstein, G. Survey of functional activities of alpha-fetoprotein derived growth inhibitory peptides: Review and prospects Curr. Protein Pept. Sci. 2006, 7, 73-100
7. Mizejewski, G. J.; Eisele, L.; Maccoll, R. Anticancer versus antigrowth activities of three analogs of the growth-inhibitory peptide: Relevance to physicochemical properties Anticancer Res. 2006, 26, 3071-3076
8. Sierralta, W. D.; Epunan, M. J.; Reyes, J. M.; Valladares, L. E.; Andersen, T. T.; Bennett, J. A.; Jacobson, H. I.; Pino, A. M. A peptide derived from alpha-fetoprotein inhibits the proliferation induced by estradiol in mammary tumor cells in culture Oncol. Rep. 2008, 19, 229-235
9. Mizejewski, G. Mechanism of Cancer Growth Suppression of Alpha-Fetoprotein Derived Growth Inhibitory Peptides (GIP): Comparison of GIP-34 versus GIP-8 (AFPep). Updates and Prospects Cancers 2011, 3, 2709-2733
10. Richardson, B. E.; Hulka, B. S.; Peck, J. L. D.; Hughes, C. L.; van den Berg, B. J.; Christianson, R. E.; Calvin, J. A. Levels of maternal serum alpha-fetoprotein (AFP) in pregnant women and subsequent breast cancer risk Am. J. Epidemiol. 1998, 148, 719-727
11. Mesfin, F. B.; Bennett, J. A.; Jacobson, H. I.; Zhu, S. J.; Andersen, T. T. Alpha-fetoprotein-derived antiestrotrophic octapeptide Biochim. Biophys. Acta 2000, 1501, 33-43
12. Bennett, J. A.; Mesfin, F. B.; Andersen, T. T.; Gierthy, J. F.; Jacobson, H. I. A peptide derived from alpha-fetoprotein prevents the growth of estrogen-dependent human breast cancers sensitive and resistant to tamoxifen Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2211-2215
13. DeFreest, L. A.; Mesfin, F. B.; Joseph, L.; McLeod, D. J.; Stallmer, A.; Reddy, S.; Balulad, S. S.; Jacobson, H. I.; Andersen, T. T.; Bennett, J. A. Synthetic peptide derived from alpha-fetoprotein inhibits growth of human breast cancer: investigation of the pharmacophore and synthesis optimization J. Pept. Res. 2004, 63, 409-419
14. Kirschner, K. N.; Lexa, K. W.; Salisburg, A. M.; Alser, K. A.; Joseph, L.; Andersen, T. T.; Bennett, J. A.; Jacobson, H. I.; Shields, G. C. Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein J. Am. Chem. Soc. 2007, 129, 6263-6268
15. Lexa, K. W.; Alser, K. A.; Salisburg, A. M.; Ellens, D. J.; Hernandez, L.; Bono, S. J.; Michael, H. C.; Derby, J. R.; Skiba, J. G.; Feldgus, S. The search for low energy conformational families of small peptides: Searching for active conformations of small peptides in the absence of a known receptor Int. J. Quantum Chem. 2007, 107, 3001-3012
16. Joseph, L. C.; Bennett, J. A.; Kirschner, K. N.; Shields, G. C.; Hughes, J.; Lostritto, N.; Jacobson, H. I.; Andersen, T. T. Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein J. Pept. Sci. 2009, 15, 319-325
17. Shields, G. C. Computational approaches for the design of peptides with anti-breast cancer properties Future Med. Chem. 2009, 1, 201-212
18. Schlick, T.; Collepardo-Guevara, R.; Halvorsen, L. A.; Jung, S.; Xiao, X. Biomolecular modeling and simulation: a field coming of age Q. Rev. Biophys. 2011, 44, 191-228
19. Wüthrich, K. NMR of Proteins and Nucleic Acids; John Wiley & Sons, Ltd: New York, 2001.
20. Rienstra, C. M.; Tucker-Kellogg, L.; Jaroniec, C. P.; Hohwy, M.; Reif, B.; McMahon, M. T.; Tidor, B.; Lozano-Perez, T.; Griffin, R. G. De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10260-10265
21. Kendrew, J. C.; Bodo, G.; Dintzis, H. M.; Parrish, R. G.; Wyckoff, H.; Phillips, D. C. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis Nature 1958, 181, 662-666
22. Schultz, S. C.; Shields, G. C.; Steitz, T. A. Crystallization of Escherichia coli Catabolite Gene Activator Protein with its DNA Binding Site: The Use of Modular DNA J. Mol. Biol. 1990, 213, 159-166
23. Schultz, S. C.; Shields, G. C.; Steitz, T. A. Crystal Structure of a CAP-DNA Complex: The DNA Is Bent by 90 Degrees Science 1991, 253, 1001-1007
24. Schroder, G. F.; Levitt, M.; Brunger, A. T. Super-resolution biomolecular crystallography with low-resolution data Nature 2010, 464, 1218-1222
25. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray ionization for mass spectrometry of large biomolecules Science 1989, 246, 64-71
26. Yates, J. R. A century of mass spectrometry: From atoms to proteomes Nat. Methods 2011, 8, 633-637
27. Cramer, C. J.; Truhlar, D. G. AM1-SM2 AND PM3-SM3 parametrized SCF solvation models for free energies in aqueous solution J. Comput.-Aided Mol. Des. 1992, 6, 629-666
28. Klamt, A.; Schuurmann, 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
29. Andzelm, J.; Kolmel, C.; Klamt, A. Incorporation of solvent effects into density functional calculations of molecular energies and geometries J. Chem. Phys. 1995, 103, 9312-9320
30. 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
31. Cances, 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
32. Barone, V.; Cossi, M.; Tomasi, J. A new definition of cavities for the computation of solvation free energies by the polarizable continuum model J. Chem. Phys. 1997, 107, 3210-3221
33. Barone, V.; Cossi, M.; Tomasi, J. Geometry optimization of molecular structures in solution by the polarizable continuum model J. Comput. Chem. 1998, 19, 404-417
34. Cramer, C. J.; Truhlar, D. G. Implicit solvation models: Equilibria, structure, spectra, and dynamics Chem. Rev. 1999, 99, 2161-2200
35. Thompson, J. D.; Cramer, C. J.; Truhlar, D. G. New universal solvation model and comparison of the accuracy of the SM5.42R, SM5.43R, C-PCM, D-PCM, and IEF-PCM continuum solvation models for aqueous and organic solvation free energies and for vapor pressures J. Phys. Chem. A 2004, 108, 6532-6542
36. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models, 2 nd ed.; Wiley: Chichester, U.K., 2004.
37. 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
38. Tomasi, J.; Mennucci, B.; Cammi, R. Quantum mechanical continuum solvation models Chem. Rev. 2005, 105, 2999-3093
39. Caricato, M.; Ingrosso, F.; Mennucci, B.; Tomasi, J. A time-dependent polarizable continuum model: Theory and application J. Chem. Phys. 2005, 122 154501
40. Curutchet, C.; Orozco, M.; Luque, F.; Mennucci, B.; Tomasi, J. Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model J. Comput. Chem. 2006, 27, 1769-1780
41. Iozzi, M.; Cossi, M.; Improta, R.; Rega, N.; Barone, V. A polarizable continuum approach for the study of heterogeneous dielectric environments J. Chem. Phys. 2006, 124 184103
42. Cramer, C. J.; Truhlar, D. G. A universal approach to solvation modeling Acc. Chem. Res. 2008, 41, 760-768
43. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening J. Chem. Theory Comput. 2009, 5, 2447-2464
44. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions J. Phys. Chem. B 2009, 113, 6378-6396
45. Sherer, E. C.; Yang, G.; Turner, G. M.; Shields, G. C.; Landry, D. W. Comparison of experimental and theoretical structures of a transition state analogue used for the induction of anti- cocaine catalytic antibodies J. Phys. Chem. A 1997, 101, 8526-8529
46. Shields, G. C.; Laughton, C. A.; Orozco, M. Molecular dynamics simulations of the d(T·A·T) triple helix J. Am. Chem. Soc. 1997, 119, 7463-7469
47. Shields, G. C.; Laughton, C. A.; Orozco, M. Molecular dynamics simulation of a PNA·DNA·PNA triple helix in aqueous solution J. Am. Chem. Soc. 1998, 120, 5895-5904
48. Sherer, E. C.; Bono, S. J.; Shields, G. C. Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond J. Phys. Chem. B 2001, 105, 8445-8451
49. Shea, J. E.; Brooks, C. L., III from Folding Theories to Folding Proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding Annu. Rev. Phys. Chem. 2001, 52, 499-535
50. Gogonea, V.; Westerhoff, L. M.; Merz, K. M. Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrodinger equation for large molecular systems using a composite density functional-semiempirical Hamiltonian J. Chem. Phys. 2000, 113, 5604-5613
51. Van der Vaart, A.; Gogonea, V.; Dixon, S. L.; Merz, K. M. Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method J. Comput. Chem. 2000, 21, 1494-1504
52. van der Vaart, A.; Suarez, D.; Merz, K. M. Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems J. Chem. Phys. 2000, 113, 10512-10523
53. Simmerling, C.; Strockbine, B.; Roitberg, A. E. All-atom structure prediction and folding simulations of a stable protein J. Am. Chem. Soc. 2002, 124, 11258-11259
54. Estiu, G.; Merz, K. M. Enzymatic catalysis of urea decomposition: Elimination or hydrolysis? J. Am. Chem. Soc. 2004, 126, 11832-11842
55. Crespo, A.; Marti, M. A.; Estrin, D. A.; Roitberg, A. E. Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase J. Am. Chem. Soc. 2005, 127, 6940-6941
56. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
57. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920
58. Estiu, G.; Suarez, D.; Merz, K. M., Jr. Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases J. Comput. Chem. 2006, 27, 1240-1262
59. Wollacott, A. M.; Merz, K. M., Jr. Assessment of semiempirical quantum mechanical methods for the evaluation of protein structures J. Chem. Theory Comput. 2007, 3, 1609-1619
60. Wickstrom, L.; Bi, Y.; Hornak, V.; Raleigh, D. P.; Simmerling, C. Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: Molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction Biochemistry 2007, 46, 3624-3634
61. Ding, F.; Layten, M.; Simmerling, C. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments J. Am. Chem. Soc. 2008, 130, 7184-7185
62. Okur, A.; Wickstrom, L.; Simmerling, C. Evaluation of salt bridge structure and energetics in peptides using explicit, implicit, and hybrid solvation models J. Chem. Theory Comput. 2008, 4, 488-498
63. Mart, M. A.; Lebrero, M. C. G.; Roitberg, A. E.; Estrin, D. A. Bond or cage effect: How nitrophorins transport and release nitric oxide J. Am. Chem. Soc. 2008, 130, 1611-1618
64. Demir, O.; Roitberg, A. E. Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase Biochemistry 2009, 48, 3398-3406
65. Seabra, G. d. M.; Walker, R. C.; Roitberg, A. E. Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective J. Phys. Chem. A 2009, 113, 11938-11948
66. Wang, X. S.; Roitberg, A. E.; Richards, N. G. J. Computational Studies of Ammonia Channel Function in Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase Biochemistry 2009, 48, 12272-12282
67. He, X.; Fusti-Molnar, L.; Cui, G.; Merz, K. M., Jr. Importance of Dispersion and Electron Correlation in ab Initio Protein Folding J. Phys. Chem. B 2009, 113, 5290-5300
68. Galiano, L.; Ding, F.; Veloro, A. M.; Blackburn, M. E.; Simmerling, C.; Fanucci, G. E. Drug Pressure Selected Mutations in HIV-1 Protease Alter Flap Conformations J. Am. Chem. Soc. 2009, 131, 430-431
69. Sun, L.; Simmerling, C.; Ojima, I. Recent Advances in the Study of the Bioactive Conformation of Taxol ChemMedChem. 2009, 4, 719-731
70. Sindhikara, D. J.; Roitberg, A. E.; Merz, K. M., Jr. Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations Biochemistry 2009, 48, 12024-12033
71. He, X.; Merz, K. M., Jr. Divide and Conquer Hartree-Fock Calculations on Proteins J. Chem. Theory Comput. 2010, 6, 405-411
72. Faver, J. C.; Benson, M. L.; He, X.; Roberts, B. P.; Wang, B.; Marshall, M. S.; Sherrill, C. D.; Merz, K. M. The Energy Computation Paradox and ab initio Protein Folding PLoS One 2011, 6 e18868
73. Rodriguez Limardo, R. G.; Ferreiro, D. N.; Roitberg, A. E.; Marti, M. A.; Turjanski, A. G. p38 gamma Activation Triggers Dynamical Changes in Allosteric Docking Sites Biochemistry 2011, 50, 1384-1395
74. Bergonzo, C.; Campbell, A. J.; de los Santos, C.; Grollman, A. P.; Simmerling, C. Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase J. Am. Chem. Soc. 2011, 133, 14504-14506
75. Pierdominici-Sottile, G.; Horenstein, N. A.; Roitberg, A. E. Free Energy Study of the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase. From the Michaelis Complex to the Covalent Intermediate Biochemistry 2011, 50, 10150-10158
76. Chakravorty, D. K.; Wang, B.; Lee, C. W.; Giedroc, D. P.; Merz, K. M., Jr. Simulations of Allosteric Motions in the Zinc Sensor CzrA J. Am. Chem. Soc. 2012, 134, 3367-3376
77. Shang, Y.; Simmerling, C. Molecular Dynamics Applied in Drug Discovery: The Case of HIV-1 Protease. In Computational Drug Discovery and Design; Baron, R., Ed.; Methods in Molecular Biology; Humana Press Inc: Totowa, NJ, 2012; Vol. 819; pp 527-549.
78. Fu, Z.; Li, X.; Merz, K. M. Conformational Analysis of Free and Bound Retinoic Acid J. Chem. Theory Comput. 2012, 8, 1436-1448
79. Roberts, B. P.; Miller, B. R.; Roitberg, A. E.; Merz, K. M. Wide-Open Flaps Are Key to Urease Activity J. Am. Chem. Soc. 2012, 134, 9934-9937
80. Boechi, L.; Arrar, M.; Marti, M. A.; Olson, J. S.; Roitberg, A. E.; Estrin, D. A. Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7 J. Biol. Chem. 2013, 288, 6754-6762
81. Swails, J. M.; Roitberg, A. E. Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics J. Chem. Theory Comput. 2012, 8, 4393-4404
82. Mulholland, A. J.; Roitberg, A. E.; Tuñón, I. Enzyme dynamics and catalysis in the mechanism of DNA polymerase Theor. Chem. Acc. 2012, 131, 1-4
83. Miller, B. R.; McGee, T. D.; Swails, J. M.; Homeyer, N.; Gohlke, H.; Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations J. Chem. Theory Comput. 2012, 8, 3314-3321
84. as: The Case of Nitrophorin 4 PLoS Comput. Biol. 2012, 8 e1002761
85. Dashti, D. S.; Meng, Y. L.; Roitberg, A. E. pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method J. Phys. Chem. B 2012, 116, 8805-8811
86. Chakravorty, D. K.; Parker, T. M.; Guerra, A. J.; Sherrill, C. D.; Giedroc, D. P.; Merz, K. M. Energetics of Zinc-Mediated Interactions in the Allosteric Pathways of Metal Sensor Proteins J. Am. Chem. Soc. 2013, 135, 30-33
87. Fu, Z.; Li, X.; Miao, Y. P.; Merz, K. M. Conformational Analysis and Parallel QM/MM X-ray Refinement of Protein Bound Anti-Alzheimer Drug Donepezil J. Chem. Theory Comput. 2013, 9, 1686-1693
88. Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Reversible peptide folding in solution by molecular dynamics simulation J. Mol. Biol. 1998, 280, 925-932
89. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Peptide Folding: When Simulation Meets Experiment Angew. Chem., Int. Ed. 1999, 38, 236-240
90. Simmerling, C.; Strockbine, B.; Roitberg, A. E. All-atom structure prediction and folding simulations of a stable protein J. Am. Chem. Soc. 2002, 124, 11258-11259
91. Qiu, L. L.; Pabit, S. A.; Roitberg, A. E.; Hagen, S. J. Smaller and faster: The 20-residue Trp-cage protein folds in 4 mu s J. Am. Chem. Soc. 2002, 124, 12952-12953
92. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26, 1668-1688
93. Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 2000, 104, 3712-3720
94. Bernholdt, D. E.; Harrison, R. J. Large-scale correlated electronic structure calculations: The RI-MP2 method on parallel computers Chem. Phys. Lett. 1996, 250, 477-484
95. Weigend, F.; Haser, M. RI-MP2: First derivatives and global consistency Theor. Chem. Acc. 1997, 97, 331-340
96. Werner, H. J.; Manby, F. R.; Knowles, P. J. Fast linear scaling second-order Møller-Plesset perturbation theory (MP2) using local and density fitting approximations J. Chem. Phys. 2003, 118, 8149-8160
97. Marshall, M. S.; Sears, J. S.; Burns, L. A.; Bredas, J. L.; Sherrill, C. D. An Error and Efficiency Analysis of Approximations to Møller-Plesset Perturbation Theory J. Chem. Theory Comput. 2010, 6, 3681-3687
98. Temelso, B.; Archer, K. A.; Shields, G. C. Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections J. Phys. Chem. A 2011, 115, 12034-12046
99. Pérez, C.; Muckle, M. T.; Zaleski, D. P.; Seifert, N. A.; Temelso, B.; Shields, G. C.; Kisiel, Z.; Pate, B. H. Structures of Cage, Prism, and Book Isomers of Water Hexamer from Broadband Rotational Spectroscopy Science 2012, 336, 897-901
100. Pérez, C.; Lobsiger, S.; Seifert, N. A.; Zaleski, D. P.; Temelso, B.; Shields, G. C.; Kisiel, Z.; Pate, B. H. Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer Chem. Phys. Lett. 2013, 571, 1-15
101. Stewart, J. J. P. Optimization of parameters for semiempirical methods. I. Method J. Comput. Chem. 1989, 10, 209-220
102. Optimization of parameters for semiempirical methods. II. Applications. J. Comput. Chem. 1989, 10, 221-264.
103. Stewart, J. J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213
104. Stewart, J. J. P. Application of the PM6 method to modeling proteins J. Mol. Model. 2009, 15, 765-805
105. Rezac, J.; Fanfrlik, J.; Salahub, D.; Hobza, P. Semiempirical Quantum Chemical PM6Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes J. Chem. Theory Comput. 2009, 5, 1749-1760
106. Korth, M.; Pitonak, M.; Rezac, J.; Hobza, P. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods J. Chem. Theory Comput. 2010, 6, 344-352
107. Jurema, M. W.; Shields, G. C. Ability of the PM3 Quantum Mechanical Method to Model Inter molecular Hydrogen Bonding between Neutral Molecules J. Comput. Chem. 1993, 14, 89-104
108. Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen J. Chem. Phys. 1989, 90, 1007-1023
109. Tao, J.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids Phys. Rev. Lett. 2003, 91 146401
110. Adamo, C.; Barone, V. Toward reliable density functional methods without adjustable parameters: The PBE0 model J. Chem. Phys. 1999, 110, 6158-6170
111. Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals Theor. Chem. Acc. 2008, 120, 215-241
112. Neese, F.; Wennmohs, F.; Hansen, A.; Becker, U. Efficient, approximate and parallel Hartree-Fock and hybrid DFT calculations. A 'chain-of-spheres' algorithm for the Hartree-Fock exchange Chem. Phys. 2009, 356, 98-109
113. Kossmann, S.; Neese, F. Comparison of two efficient approximate Hartee-Fock approaches Chem. Phys. Lett. 2009, 481, 240-243
114. Kossmann, S.; Neese, F. Efficient Structure Optimization with Second-Order Many-Body Perturbation Theory: The RIJCOSX-MP2Method J. Chem. Theory Comput. 2010, 6, 2325-2338
115. Neese, F. The ORCA program system Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 73-78
116. Grimme, S. Accurate description of van der Waals complexes by density functional theory including empirical corrections J. Comput. Chem. 2004, 25, 1463-1473
117. Jurečka, P.; Černý, J.; Hobza, P.; Salahub, D. R. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations J. Comput. Chem. 2007, 28, 555-569
118. Sherrill, C. D. Frontiers in electronic structure theory J. Chem. Phys. 2010, 132, 7
119. Marom, N.; Tkatchenko, A.; Rossi, M.; Gobre, V. V.; Hod, O.; Scheffler, M.; Kronik, L. Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals J. Chem. Theory Comput. 2011, 7, 3944-3951
120. Hujo, W.; Grimme, S. Performance of the van der Waals Density Functional VV10 and (hybrid)GGA Variants for Thermochemistry and Noncovalent Interactions J. Chem. Theory Comput. 2011, 7, 3866-3871
121. Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction J. Comput. Chem. 2006, 27, 1787-1799
122. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu J. Chem. Phys. 2010, 132 154104
123. Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory J. Comput. Chem. 2011, 32, 1456-1465
124. Meissner, T.; Wentz, F. J. The complex dielectric constant of pure and sea water from microwave satellite observations IEEE Geosci. Remote Sens. Lett. 2004, 42, 1836-1849
125. Stewart, J. J. P. MOPAC2012 Computational Chemistry, http://OpenMOPAC.net (2012). In MOPAC, 2009 ed.; Colorado Springs, CO, USA, 2008.
126. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision D.01; Gaussian, Inc.: Wallingford, CT, 2009.
127. Day, M. B.; Kirschner, K. N.; Shields, G. C. Global search for minimum energy (H2O)21H+ clusters, n=3-5 J. Phys. Chem. A 2005, 109, 6773-6778
128. 2O)(n=1-4) clusters J. Chem. Phys. 2007, 126 154320
129. Hartt, G. M.; Shields, G. C.; Kirschner, K. N. Hydration of OCS with one to four water molecules in atmospheric and laboratory conditions J. Phys. Chem. A 2008, 112, 4490-4495
130. Morrell, T. E.; Shields, G. C. Atmospheric Implications for Formation of Clusters of Ammonium and 1-10 Water Molecules J. Phys. Chem. A 2010, 114, 4266-4271
131. n=2-10 J. Phys. Chem. A 2010, 114, 11725-11737
132. Husar, D. E.; Temelso, B.; Ashworth, A. L.; Shields, G. C. Hydration of the Bisulfate Ion: Atmospheric Implications J. Phys. Chem. A 2012, 116, 5151-5163
133. Temelso, B.; Morrell, T. E.; Shields, R. M.; Allodi, M. A.; Wood, E. K.; Kirschner, K. N.; Castonguay, T. C.; Archer, K. A.; Shields, G. C. Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications J. Phys. Chem. A 2012, 116, 2209-2224
134. Temelso, B.; Phan, T. N.; Shields, G. C. Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation J. Phys. Chem. A 2012, 116, 9745-9758
135. Zheng, Y.; Merz, K. M., Jr. Study of hydrogen bonding interactions relevant to biomolecular structure and function J. Comput. Chem. 1992, 13, 1151-1169
136. + with the PM3 Quantum-Mechanical Method J. Comput. Chem. 1993, 14, 1326-1332
137. Kirschner, K. N.; Shields, G. C. Quantum-Mechanical Investigation of Large Water Clusters Int. J. Quantum Chem. 1994, 349-360
138. Lively, T. N.; Jurema, M. W.; Shields, G. C. Hydrogen Bonding of Nucleotide Base Pairs: Application of the PM3Method Int. J. Quantum Chem. 1994, 95-107
139. Sherer, E. C.; York, D. M.; Cramer, C. J. Fast approximate methods for calculating nucleic acid base pair interaction energies J. Comput. Chem. 2003, 24, 57-67
140. Beccara, S. A.; Faccioli, P.; Sega, M.; Pederiva, F.; Garberoglio, G.; Orland, H. Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations J. Chem. Phys. 2011, 134 024501
141. Valdes, H.; Pluháčková, K.; Pitonák, M.; Rezáč, J.; Hobza, P. Benchmark database on isolated small peptides containing an aromatic side chain: Comparison between wave function and density functional theory methods and empirical force field Phys. Chem. Chem. Phys. 2008, 10, 2747-2757
142. Riley, K. E.; Pitonak, M.; Jurecka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories Chem. Rev. 2010, 110, 5023-5063
143. Zhou, R.; Berne, B. J.; Germain, R. The free energy landscape for β hairpin folding in explicit water Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14931
144. Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C. Investigation of salt bridge stability in a generalized born solvent model J. Chem. Theory Comput 2006, 2, 115-127
145. Chou, K. Prediction of Tight Turns and Their Types in Proteins Anal. Biochem. 2000, 286, 1-16
146. Burns, L. A.; Mayagoitia, A. V.; Sumpter, B. G.; Sherrill, C. D. Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals J. Chem. Phys. 2011, 134 084107
147. Hao, P.; Sun, J.; Xiao, B.; Ruzsinszky, A.; Csonka, G. I.; Tao, J.; Glindmeyer, S.; Perdew, J. P. Performance of meta-GGA Functionals on General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions J. Chem. Theory Comput. 2012, 9, 355-363
148. Zhao, Y.; Truhlar, D. G. Density Functional Theory for Reaction Energies: Test of Meta and Hybrid Meta Functionals, Range-Separated Functionals, and Other High-Performance Functionals J. Chem. Theory Comput. 2011, 7, 669-676