High-throughput calculations of molecular properties in the MedeA environment: Accuracy of PM7 in predicting vibrational frequencies, ideal gas entropies, heat capacities, and gibbs free energies of organic molecules

Journal of Chemical and Engineering Data

Volumn 59, Issue 10, 2014, Pages 3136-3143

  Rozanska, Xavier ^a   Stewart, James J P ^b   Ungerer, Philippe ^a   Leblanc, Benoit ^a   Freeman, Clive ^c   Saxe, Paul ^c   Wimmer, Erich ^a  

^a Materials Design Sarl   (France)

^b Stewart Computational Chemistry   (United States)

^c Materials Design Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH-THROUGHPUT; IDEAL GAS; MOLECULAR PROPERTIES; ORGANIC MOLECULES;

EID: 84907899599     PISSN: 00219568     EISSN: 15205134     Source Type: Journal    
DOI: 10.1021/je500201y     Document Type: Article

References (42)

1. Van Speybroeck, V.; Gani, R.; Meier, R. J. The calculation of thermodynamic properties of molecules Chem. Soc. Rev. 2010, 39, 1764-1779
2. European Chemicals Agency. Pre-registered Substances; ECHA: Helsinki, Finland, http://echa.europa.eu/en/information-on-chemicals/pre-registered-substances, 2013.
3. MedeA: Materials Exploration and Design Analysis, version 2.14.6; Material Design, Inc.: Angel Fire, NM, 1998-2014; http://www.materialsdesign.com.
4. East, A. L. L.; Radom, L. Ab initio statistical thermodynamical models for the computation of third-law entropies J. Chem. Phys. 1997, 106, 6655-6674
5. Guthrie, J. P. Use of DFT methods for the calculation of the entropy of gas phase organic molecules: An examination of the quality of results from a simple approach J. Phys. Chem. A 2001, 105, 8495-8499
6. Marriott, R. A.; White, M. A. Comparison of ab initio and group additive ideal gas heat capacities AIChE J. 2005, 51, 292-297
7. DeTar, D. F. Calculation of entropy and heat capacity of organic compounds in the gas phase. Evaluation of a consistent method without adjustable parameters. Applications to hydrocarbons J. Phys. Chem. A 2007, 111, 4464-4477
8. Vansteenkiste, P.; Van Speybroeck, V.; Marin, G. B.; Waroquier, M. Ab initio calculation of entropy and heat capacity of gas-phase n -alkanes using internal rotations J. Phys. Chem. A 2003, 107, 3139-3145
9. Pfaendtner, J.; Yu, X.; Broadbelt, L. J. The 1-D hindered rotor approximation Theor. Chem. Acc. 2007, 118, 881-898
10. Alecu, I. M.; Zheng, J.; Zhao, Y.; Truhlar, D. G. Computational thermochemistry: Scale factor databases and scale factors for vibrational frequencies obtained from electronic model chemistries J. Chem. Theory Comput. 2010, 6, 2872-2887
11. Neugebauer, J.; Hess, B. A. Fundamental vibrational frequencies of small polyatomic molecules from density-functional calculations and vibrational perturbation theory J. Chem. Phys. 2003, 118, 7215-7225
12. Reiher, M.; Brehm, G.; Schneider, S. Assignment of vibrational spectra of 1,10-phenanthroline by comparison with frequencies and Raman intensities from density functional calculations J. Phys. Chem. A 2004, 108, 734-742
13. CÌŒervinka, C.; Fulem, M.; RuÌŠzÌŒicÌŒka, K. Evaluation of accuracy of ideal-gas heat capacity and entropy calculations by density functional theory (DFT) for rigid molecules J. Chem. Eng. Data 2012, 57, 227-232
14. CÌŒervinka, C.; Fulem, M.; RuÌŠzÌŒicÌŒka, K. Evaluation of uncertainty of ideal-gas entropy and heat capacity calculations by density functional theory (DFT) for molecules containing symmetrical internal rotors J. Chem. Eng. Data 2013, 58, 1382-1390
15. +: Experiment and theory in concert Angew. Chem., Int. Ed. 2006, 45, 4677-4681
16. Rozanska, X.; Vuilleumier, R. Mechanisms of the water gas shift reaction by iron pentacarbonyl in the gas phase Inorg. Chem. 2008, 47, 8635-8640
17. 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
18. Stewart, J. J. P. Optimization of parameters for semiempirical methods VI: More modifications to the NDDO approximations and re-optimization of parameters J. Mol. Model. 2013, 19, 1-32
19. Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
20. DIADEM: The DIPPR Information and Data Evaluation Manager for the Design Institute for Physical Properties, version 6.0.0; AIChE: New York, 2011.
21. NIST Standard Reference Database Number 69. NIST Chemistry WebBook; Mallard, W. G.; Linstrom, P. J., Eds.; National Institute of Standards and Technology: Gaithersburg, MD, 2011; http://webbook.nist.gov.
22. The Properties of Gases and Liquids, 5th Int. ed.; Poling, B. E.; Prausnitz, J. M.; Oa'Connell, J. P., Eds.; McGraw-Hill: Boston, MA, 2007; pp A.35-A.46.
23. Oa'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeesch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Chem. Inf. 2011, 3, 33
24. Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations J. Am. Chem. Soc. 1992, 114, 10024-10039
25. Stewart, J. J. P. MOPAC2012; Stewart Computational Chemistry: Colorado Springs, CO, 2012; http://OpenMOPAC.net.
26. Ahlrichs, R.; Baer, M.; Haeser, M.; Horn, H.; Koelmel, C. Electronic structure calculation on workstation computers: The program system turbomole Chem. Phys. Lett. 1989, 162, 165-169
27. Treutler, O.; Ahlrichs, R. Efficient molecular numerical integration scheme J. Chem. Phys. 1995, 102, 346-354
28. Deglmann, P.; Furche, F.; Ahlrichs, R. An efficient implementation of second analytical derivatives for density functional methods Chem. Phys. Lett. 2002, 362, 511-518
29. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 1988, 38, 3098-3100
30. Perdew, J. P. Density-functional approximation for the correlation energy of the inhomogeneous electron gas Phys. Rev. B 1986, 33, 8822-8824
31. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 1988, 37, 785-789
32. Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648-5652
33. Schaefer, A.; Huber, C.; Alhrichs, R. Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr J. Chem. Phys. 1994, 100, 5829-5835
34. Merrick, J. P.; Moran, D.; Radom, L. An evaluation of harmonic vibrational frequency scale factors J. Phys. Chem. A 2007, 111, 11683-11700
35. Ditchfield, R.; Hehre, W. J.; Pople, J. A. Self-consistent molecular-orbital methods. IX An extended Gaussian-type basis for molecular-orbital studies of organic molecules J. Chem. Phys. 1971, 54, 724-728
36. Advances in Chemical Physics, New Methods in Computational Quantum Mechanics; Prigogine, J.; Rice, S. A., Eds.; John Wiley & Sons: New York, 1996; pp 713-714.
37. Training set of the Estimation Program Interface (EPI) Suite; EPAa's Office of Pollution Prevention Toxics and Syracuse Research Corporation (SRC): Syracuse, NY, 2000-2012.
38. Plimpton, S. Fast parallel algorithms for short-range molecular dynamics J. Comput. Phys. 1995, 117, 1-19
39. Kresse, G.; Hafner, J. Ab initio molecular dynamics for liquid metals Phys. Rev. B 1993, 47, 558-561
40. Kresse, G.; Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium Phys. Rev. B 1994, 49, 14251-14269
41. Kresse, G.; FurthmuÌller, F. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set Comput. Mater. Sci. 1996, 6, 15-50
42. Kresse, G.; FurthmuÌller, F. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set Phys. Rev. B 1996, 54, 11169-11186