Erratum: Application of molecular dynamics simulations in molecular property prediction. 1. Density and heat of vaporization (Journal of Chemical Theory and Computation (2011) 7 DOI: 10.1021/ct200142z);Application of molecular dynamics simulations in molecular property prediction. 1. Density and heat of vaporization

Journal of Chemical Theory and Computation

Volumn 7, Issue 7, 2011, Pages 2151-2165

  Wang, Junmei ^a   Hou, Tingjun ^b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b SOOCHOW UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79960216924     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct2004287     Document Type: Erratum

References (66)

1. Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 2002, 9, 646-652 (Pubitemid 34977295)
2. van Gunsteren, W. F.; Mark, A. E. Validation of molecular dynamics simulation J. Chem. Phys. 1998, 108, 6109-6116 (Pubitemid 128576235)
3. Foloppe, N.; MacKerell, A. D. J. All-atom empirical force field for nucleic acids. 1) Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21, 86-104
4. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 1998, 102, 3586-3616 (Pubitemid 128576688)
5. 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
6. Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074
7. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 (Pubitemid 26399746)
8. Oostenbrink, C.; Soares, T. A.; van der Vegt, N. F.; van Gunsteren, W. F. Validation of the 53A6 GROMOS force field Eur. Biophys. J. 2005, 34, 273-284 (Pubitemid 40884072)
9. Soares, T. A.; Hunenberger, P. H.; Kastenholz, M. A.; Krautler, V.; Lenz, T.; Lins, R. D.; Oostenbrink, C.; van Gunsteren, W. F. An improved nucleic acid parameter set for the GROMOS force field J. Comput. Chem. 2005, 26, 727-737
10. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
11. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges- the RESP model J. Phys. Chem. 1993, 97, 10269-10280
12. Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. Application of the multimolecule and multiconformational RESP methodology to biopolymers- charge derivation for DNA, RNA, and proteins J. Comput. Chem. 1995, 16, 1357-1377
13. Caldwell, J. W.; Kollman, P. A. Structure and Properties of Neat Liquids Using Nonadditive Molecular-Dynamics-Water, Methanol, and N-Methylacetamide J. Phys. Chem. 1995, 99, 6208-6219
14. Fox, T.; Kollman, P. A. Application of the RESP methodology in the parametrization of organic solvents J. Phys. Chem. B 1998, 102, 8070-8079 (Pubitemid 128578425)
15. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast efficient generation of high quality atomic charges. AM1-BCC model: I. method J. Comput. Chem. 2000, 21, 132-146
16. Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641 (Pubitemid 35330860)
17. Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and use of the MM-PBSA approach for drug discovery J. Med. Chem. 2005, 48, 4040-4048 (Pubitemid 40800612)
18. Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations J. Chem. Inf. Model. 2011, 51, 69-82
19. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5, 350-358
20. MacKerell, A. D.; Shim, J. H.; Anisimov, V. M. Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide J. Chem. Theory Comput. 2008, 4, 1307-1312
21. Physical constants of organic compounds. In CRC Handbook of Chemistry and Physics, 86 th ed.; Lide, D. R. E., Eds.; CRC Press: Boca Raton, FL, 2005; pp 1-3.
22. Siepmann, J. I.; Karaborni, S.; Smit, B. Simulating the Critical-Behavior of Complex Fluids Nature 1993, 365, 330-332
23. Enthalpies of Vaporization of Organic Compounds: A Critical Review and Data Compilation; Majer, V.; Svoboda, V., Eds.; Blackwell Scientific Publications: Oxford, U. K., 1985; pp 1-304.
24. Kemp, J. D.; Egan, C. J. Hindered Rotation of the Methyl Groups in Propane. The Heat Capacity, Vapor Pressure, Heats of Fusion and Vaporization of Propane. Entropy and Density of the Gas J. Am. Chem. Soc. 1938, 60, 1521-1525
25. Pedley, J. B.; Naylor, R. D.; Kirby, S. P. Thermochemical Data of Organic Compounds, 2 nd ed.; Chapman and Hall: New York, 1986; pp 1-792.
26. Wiberg, K. B.; Crocker, L. S.; Morgan, K. M. Thermochemical Studies of Carbonyl-Compounds 0.5. Enthalpies of Reduction of Carbonyl Groups J. Am. Chem. Soc. 1991, 113, 3447-3450
27. Geller, B. E. Properties of the dimethylformamide water system. I. Thermochemical properties Russ. J. Phys. Chem. 1961, 35, 542-564
28. Pihlaja, K.; Heikklia, J. Enthalpies of formation of cyclic acetals. 1,3-dioxolane, 2-methyl-1,3-dioxolane, and 2,4-dimethyl-1,3-dioxolanes Acta Chem. Scand. 1969, 23, 1053-1055
29. Steele, W. V.; Archer, D. G.; Chirico, R. D.; Collier, W. B.; Hossenlopp, I. A.; Nguyen, A.; Smith, N. K.; Gammon, B. E. The thermodynamic properties of quinoline and isoquinoline J. Chem. Thermodyn. 1988, 20, 1233-1264
30. Wang, J.; Hou, T.; Xu, X. Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas J. Chem. Inf. Model. 2009, 49, 571-81
31. Konicek, J.; Wadso, I. Enthalpies of Vaporization of Organic Compounds 0.7. Some Carboxylic Acids Acta Chem. Scand. 1970, 24, 2612-2626
32. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; 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.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03; Gaussian, Inc.: Wallingford, CT, 2004.
33. Case, D. A.; Darden, T. A.; Cheatham, I.; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER10; University of California at San Francisco: San Francisco, CA, 2008.
34. Wang, J. M.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Model. 2006, 25, 247-260 (Pubitemid 44363172)
35. Darden, T.; Perera, L.; Li, L.; Pedersen, L. New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations Structure 1999, 7, R55-60
36. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593
37. Sagui, C.; Pedersen, L. G.; Darden, T. A. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations J. Chem. Phys. 2004, 120, 73-87
38. Miyamoto, S.; Kollman, P. A. Settle-an Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13, 952-962
39. Shirts, M. R.; Mobley, D. L.; Chodera, J. D.; Pande, V. S. Accurate and efficient corrections for missing dispersion interactions in molecular Simulations J. Phys. Chem. B 2007, 111, 13052-13063 (Pubitemid 350197631)
40. Uberuaga, B. P.; Anghel, M.; Voter, A. F. Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation J. Chem. Phys. 2004, 120, 6363-6374
41. Izaguirre, J. A.; Catarello, D. P.; Wozniak, J. M.; Skeel, R. D. Langevin stabilization of molecular dynamics J. Chem. Phys. 2001, 114, 2090-2098 (Pubitemid 32873171)
42. Larini, L.; Mannella, R.; Leporini, D. Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms J. Chem. Phys. 2007, 126, 104101
43. Loncharich, R. J.; Brooks, B. R.; Pastor, R. W. Langevin Dynamics of Peptides-the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N?-Methylamide Biopolymers 1992, 32, 523-535
44. Harvey, S. C.; Tan, R. K. Z.; Cheatham, T. E. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition J. Comput. Chem. 1998, 19, 726-740
45. Andersen, H. C. Molecular-Dynamics Simulations at Constant Pressure and-or Temperature J. Chem. Phys. 1980, 72, 2384-2393
46. Andrea, T. A.; Swope, W. C.; Andersen, H. C. The Role of Long Ranged Forces in Determining the Structure and Properties of Liquid Water J. Chem. Phys. 1983, 79, 4576-4584
47. Steinbrecher, T.; Mobley, D. L.; Case, D. A. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations J. Chem. Phys. 2007, 127, 214108
48. Hummer, G.; Szabo, A. Calculation of free-energy differences from computer simulations of initial and final states J. Chem. Phys. 1996, 105, 2004-2010 (Pubitemid 126612908)
49. Jorgensen, W. L.; McDonald, N. A. Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes THEOCHEM 1998, 424, 145-155 (Pubitemid 128388407)
50. McDonald, N. A.; Jorgensen, W. L. Development of an all-atom force field for heterocycles. Properties of liquid pyrrole, furan, diazoles, and oxazoles J. Phys. Chem. B 1998, 102, 8049-8059 (Pubitemid 128578423)
51. Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. L. Gas-phase and liquid-state properties of esters, nitriles, and nitro compounds with the OPLS-AA force field J. Comput. Chem. 2001, 22, 1340-1352 (Pubitemid 32900801)
52. Rizzo, R. C.; Jorgensen, W. L. OPLS all-atom model for amines: Resolution of the amine hydration problem J. Am. Chem. Soc. 1999, 121, 4827-4836 (Pubitemid 29252636)
53. Yu, H. B.; Hansson, T.; van Gunsteren, W. F. Development of a simple, self-consistent polarizable model for liquid water J. Chem. Phys. 2003, 118, 221-234
54. Price, D. J.; Brooks, C. L. A modified TIP3P water potential for simulation with Ewald summation J. Chem. Phys. 2004, 121, 10096-10103 (Pubitemid 40001663)
55. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678
56. Yu, H. B.; Geerke, D. P.; Liu, H. Y.; van Gunsteren, W. E. Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models J. Comput. Chem. 2006, 27, 1494-1504 (Pubitemid 44366225)
57. Billeter, S. R.; King, P. M.; Vangunsteren, W. F. Can the Density Maximum of Water Be Found by Computer-Simulation J. Chem. Phys. 1994, 100, 6692-6699
58. Jorgensen, W. L.; Jenson, C. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density J. Comput. Chem. 1998, 19, 1179-1186 (Pubitemid 128604734)
59. Price, D. J.; Brooks, C. L. Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA J. Comput. Chem. 2005, 26, 1529-1541 (Pubitemid 41609843)
60. Wu, X.; Brooks, B. R. Isotropic periodic sum: a method for the calculation of long-range interactions J. Chem. Phys. 2005, 122, 44107
61. Klauda, J. B.; Wu, X.; Pastor, R. W.; Brooks, B. R. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method J. Phys. Chem. B 2007, 111, 4393-400 (Pubitemid 46787633)
62. Takahashi, K.; Yasuoka, K.; Narumi, T. Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid J. Chem. Phys. 2007, 127, 114511
63. Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular Mechanics-the MM3 Force-Field for Hydrocarbons J. Am. Chem. Soc. 1989, 111, 8551-8566 (Pubitemid 20021795)
64. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An All Atom Force-Field for Simulations of Proteins and Nucleic-Acids J. Comput. Chem. 1986, 7, 230-252
65. Wang, J. M.; Cieplak, P.; Li, J.; Hou, T. J.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations I: Parameterization of Atomic Polarizability J. Phys. Chem. B 2011, 115, 3091-3099
66. Wang, J. M.; Cieplak, P.; Li, J.; Wang, J.; Cai, Q.; Hsieh, M. J.; Lei, H. X.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies J. Phys. Chem. B 2011, 115, 3100-3111