Dual-Level Method for Estimating Multistructural Partition Functions with Torsional Anharmonicity

Journal of Chemical Theory and Computation

Volumn 13, Issue 6, 2017, Pages 2511-2522

  Bao, Junwei Lucas ^a   Xing, Lili ^a   Truhlar, Donald G ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85020699775     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.7b00232     Document Type: Article

References (81)

1. Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects Phys. Rev. 1965, 140, A1133 10.1103/PhysRev.140.A1133
2. Peverati, R.; Truhlar, D. G. Quest for a universal density functional: The accuracy of density functionals across a broad spectrum of databases in chemistry and physics Philos. Trans. R. Soc., A 2014, 372, 20120476 10.1098/rsta.2012.0476
3. Gordon, M. S.; Truhlar, D. G. Scaling all correlation energy in perturbation theory calculations of bond energies and barrier heights J. Am. Chem. Soc. 1986, 108, 5412 10.1021/ja00278a007
4. Curtiss, L. A.; Raghavachari, K.; Trucks, G. W.; Pople, J. A. Gaussian-2 theory for molecular energies of first-and second-row compounds J. Chem. Phys. 1991, 94, 7221 10.1063/1.460205
5. Montgomery, J. A., Jr.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. A complete basis set model chemistry. VI. Use of density functional geometries and frequencies J. Chem. Phys. 1999, 110, 2822 10.1063/1.477924
6. Martin, J. M. L.; de Oliveira, G. Towards standard methods for benchmark quality ab initio thermochemistry-W1 and W2 theory J. Chem. Phys. 1999, 111, 1843 10.1063/1.479454
7. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. Gaussian-3 theory using scaled energies J. Chem. Phys. 2000, 112, 1125 10.1063/1.480668
8. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Doubly Hybrid Meta DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics J. Phys. Chem. A 2004, 108, 4786 10.1021/jp049253v
9. Lynch, B. J.; Truhlar, D. G. The 6-31B(d) Basis Set and the BMC-QCISD and BMC-CCSD Multicoefficient Correlation Methods J. Phys. Chem. A 2005, 109, 1643 10.1021/jp045847m
10. DeYonker, N. J.; Cundari, T. R.; Wilson, A. K. The correlation consistent composite approach (ccCA): An alternative to the Gaussian-n methods J. Chem. Phys. 2006, 124, 114104 10.1063/1.2173988
11. Karton, A.; Rabinovich, E.; Martin, J. M. L.; Ruscic, B. W4 theory for computational thermochemistry: In pursuit of confident sub-kJ/mol predictions J. Chem. Phys. 2006, 125, 144108 10.1063/1.2348881
12. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. Gaussian-4 theory J. Chem. Phys. 2007, 126, 084108 10.1063/1.2436888
13. Helgaker, T.; Klopper, W.; Tew, D. P. Quantitative quantum chemistry Mol. Phys. 2008, 106, 2107 10.1080/00268970802258591
14. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. Gn theory Wiley Interdis. Rev.: Comp. Mol, Sci. 2011, 1, 810 10.1002/wcms.59
15. Chan, B.; Radom, L. W3X: A Cost-Effective Post-CCSD(T) Composite Procedure J. Chem. Theory Comput. 2013, 9, 4769 10.1021/ct4005323
16. Raghavachari, K.; Saha, A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules Chem. Rev. 2015, 115, 5643 10.1021/cr500606e
17. -1 Accuracy J. Chem. Theory Comput. 2015, 11, 2109 10.1021/acs.jctc.5b00135
18. Seal, P.; Papajak, E.; Truhlar, D. G. Kinetics of the Hydrogen Abstraction from Carbon-3 of 1-Butanol by Hydroperoxyl Radical: Multi-Structural Variational Transition-State Calculations of a Reaction with 262 Conformations of the Transition State J. Phys. Chem. Lett. 2012, 3, 264 10.1021/jz201546e
19. Seal, P.; Truhlar, D. G. Large Entropic Effects on the Thermochemistry of Silicon Nanodusty Plasma Constituents J. Am. Chem. Soc. 2014, 136, 2786 10.1021/ja410498d
20. Seal, P.; Zheng, J.; Truhlar, D. G. Entropic Effects on the Free Energies of Clusters in Silane Plasmas J. Phys. Chem. C 2015, 119, 10085 10.1021/acs.jpcc.5b00923
21. Van Speybroeck, V.; Van Neck, D.; Waroquier, M.; Wauters, S.; Saeys, M.; Marin, G. B. Ab initio study on elementary radical reactions in coke formation Int. J. Quantum Chem. 2003, 91 (3 SPEC) 384 10.1002/qua.10458
22. 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 10.1021/jp027132u
23. Coote, M. L. The Kinetics of Addition and Fragmentation in Reversible Addition Fragmentation Chain Transfer Polymerization: An ab Initio Study J. Phys. Chem. A 2005, 109, 1230 10.1021/jp046131u
24. Bravo-Pérez, G.; Alvarez-Idaboy, J. R.; Jiménez, A. G.; Cruz-Torres, A. Quantum chemical and conventional TST calculations of rate constants for the OH + alkane reaction Chem. Phys. 2005, 310, 213 10.1016/j.chemphys.2004.10.031
25. Sabbe, M. K.; Vandeputte, A. G.; Reyniers, M.-F.; Van Speybroeck, V.; Waroquier, M.; Marin, G. B. Ab Initio Thermochemistry and Kinetics for Carbon-Centered Radical Addition and β-Scission Reactions J. Phys. Chem. A 2007, 111, 8416 10.1021/jp072897t
26. Sabbe, M. K.; Reyniers, M.-F.; Van Speybroeck, V.; Waroquier, M.; Marin, G. B. Carbon-Centered Radical Addition and β-Scission Reactions: Modeling of Activation Energies and Pre-exponential Factors ChemPhysChem 2008, 9, 124 10.1002/cphc.200700469
27. Zheng, J.; Yu, T.; Papajak, E.; Alecu, I. M.; Mielke, S. L.; Truhlar, D. G. Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: The internal-coordinate multi-structural approximation Phys. Chem. Chem. Phys. 2011, 13, 10885 10.1039/c0cp02644a
28. Yu, T.; Zheng, J.; Truhlar, D. G. Multi-structural variational transition state theory. Kinetics of the 1,4-hydrogen shift isomerization of the pentyl radical with torsional anharmonicity Chem. Sci. 2011, 2, 2199 10.1039/c1sc00225b
29. Xu, X.; Yu, T.; Papajak, E.; Truhlar, D. G. Multistructural Variational Transition State Theory: Kinetics of the Hydrogen Abstraction from Carbon-2 of 2-Methyl-1-propanol by Hydroperoxyl Radical Including All Structures and Torsional Anharmonicity J. Phys. Chem. A 2012, 116, 10480 10.1021/jp307504p
30. Alecu, I. M.; Zheng, J.; Papajak, E.; Yu, T.; Truhlar, D. G. Biofuel Combustion. Energetics and Kinetics of Hydrogen Abstraction from Carbon-1 in n-Butanol by the Hydroperoxyl Radical Calculated by Coupled Cluster and Density Functional Theories and Multistructural Variational Transition-State Theory with Multidimensional Tunneling J. Phys. Chem. A 2012, 116, 12206 10.1021/jp308460y
31. Fernández-Ramos, A. Accurate treatment of two-dimensional non-separable hindered internal rotors J. Chem. Phys. 2013, 138, 134112 10.1063/1.4798407
32. Hudzik, J. M.; Bozzelli, J. W. Calculated entropies for n-heptane, 2-methylhexane, 2,3-dimethylpentane, and radicals from the loss of H atoms Adv. Phys. Chem. 2013, 2013, 673065 10.1155/2013/673065
33. Zheng, J.; Meana-Pañâeda, R.; Truhlar, D. G. Prediction of Experimentally Unavailable Product Branching Ratios for Biofuel Combustion: The Role of Anharmonicity in the Reaction of Isobutanol with OH J. Am. Chem. Soc. 2014, 136, 5150 10.1021/ja5011288
34. Bao, J. L.; Meana-Pañâeda, R.; Truhlar, D. G. Multi-path variational transition state theory for chiral molecules: The site-dependent kinetics for abstraction of hydrogen from 2-butanol by hydroperoxyl radical, analysis of hydrogen bonding in the transition state, and dramatic temperature dependence of the activation energy Chem. Sci. 2015, 6, 5866 10.1039/C5SC01848J
35. Simón-Carballido, L.; Alves, T. V.; Dybala-Defratyka, A.; Fernández-Ramos, A. Kinetic Isotope Effects in Multipath VTST: Application to a Hydrogen Abstraction Reaction J. Phys. Chem. B 2016, 120, 1911 10.1021/acs.jpcb.5b09671
36. Bao, J. L.; Sripa, P.; Truhlar, D. G. Path-dependent variational effects and multidimensional tunneling in multi-path variational transition state theory: rate constants calculated for the reactions of HO2 with tert-butanol by including all 46 paths for abstraction at C and all six paths for abstraction at O Phys. Chem. Chem. Phys. 2016, 18, 1032 10.1039/C5CP05780A
37. Bao, J. L.; Zheng, J.; Truhlar, D. G. Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory J. Am. Chem. Soc. 2016, 138, 2690 10.1021/jacs.5b11938
38. Truhlar, D. G. A simple approximation for the vibrational partition function of a hindered internal rotation J. Comput. Chem. 1991, 12, 266 10.1002/jcc.540120217
39. Ayala, P. Y.; Schlegel, H. B. Identification and treatment of internal rotation in normal mode vibrational analysis J. Chem. Phys. 1998, 108, 2314 10.1063/1.475616
40. Zheng, J.; Truhlar, D. G. Quantum Thermochemistry: Multistructural Method with Torsional Anharmonicity Based on a Coupled Torsional Potential J. Chem. Theory Comput. 2013, 9, 1356 10.1021/ct3010722
41. Zheng, J.; Mielke, S. L.; Clarkson, K. L.; Truhlar, D. G. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity Comput. Phys. Commun. 2012, 183, 1803 10.1016/j.cpc.2012.03.007
42. Zheng, J.; Meana-Pañâeda, R.; Truhlar, D. G. MSTor version 2013: A new version of the computer code for the multi-structural torsional anharmonicity, now with a coupled torsional potential Comput. Phys. Commun. 2013, 184, 2032 10.1016/j.cpc.2013.03.011
43. Yu, T.; Zheng, J.; Truhlar, D. G. Multipath Variational Transition State Theory: Rate Constant of the 1,4-Hydrogen Shift Isomerization of the 2-Cyclohexylethyl Radical J. Phys. Chem. A 2012, 116, 297 10.1021/jp209146b
44. Vereecken, L.; Glowacki, D. R.; Pilling, M. Theoretical Chemical Kinetics in Tropospheric Chemistry: Methodologies and Applications Chem. Rev. 2015, 115, 4063 10.1021/cr500488p
45. Bao, J. L.; Zhang, X.; Truhlar, D. G. Predicting pressure-dependent unimolecular rate constants using variational transition state theory with multidimensional tunneling combined with system-specific quantum RRK theory: A definitive test for fluoroform dissociation Phys. Chem. Chem. Phys. 2016, 18, 16659 10.1039/C6CP02765B
46. Bao, J. L.; Truhlar, D. G. Silane-initiated nucleation in chemically active plasmas: validation of density functionals, mechanisms, and pressure-dependent variational transition state calculations Phys. Chem. Chem. Phys. 2016, 18, 10097 10.1039/C6CP00816J
47. Bao, J. L.; Seal, P.; Truhlar, D. G. Nanodusty plasma chemistry: A mechanistic and variational transition state theory study of the initial steps of silyl anion-silane and silylene anion-silane polymerization reactions Phys. Chem. Chem. Phys. 2015, 17, 15928 10.1039/C5CP01979F
48. Long, B.; Bao, J. L.; Truhlar, D. G. Atmospheric Chemistry of Criegee Intermediates: Unimolecular Reactions and Reactions with Water J. Am. Chem. Soc. 2016, 138, 14409 10.1021/jacs.6b08655
49. Zhao, Y.; Truhlar, D. G. Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions J. Chem. Theory Comput. 2008, 4, 1849 10.1021/ct800246v
50. Zhao, Y.; Truhlar, D. G. Density Functionals with Broad Applicability in Chemistry Acc. Chem. Res. 2008, 41, 157 10.1021/ar700111a
51. 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 10.1021/jp027132u
52. Møller, K. H.; Otkjær, R. V.; Hyttinen, N.; Kurtén, T.; Kjaergaard, H. G. Cost-Effective Implementation of Multiconformer Transition State Theory for Peroxy Radical Hydrogen Shift Reactions J. Phys. Chem. A 2016, 120, 10072 10.1021/acs.jpca.6b09370
53. Oo, C. W.; Shioji, M.; Nakao, S.; Dung, N. N.; Reksowardojo, I.; Roces, S. A.; Dugos, N. P. Ignition and combustion characteristics of various biodiesel fuels (BDFs) Fuel 2015, 158, 279 10.1016/j.fuel.2015.05.049
54. Wu, Y. G.; Lin, Y.-F.; Chang, C.-T. Combustion characteristics of fatty acid methyl esters derived from recycled cooking oil Fuel 2007, 86, 2810 10.1016/j.fuel.2007.02.029
55. Zhu, L.; Cheung, C. S.; Huang, Z. Impact of chemical structure of individual fatty acid esters on combustion and emission characteristics of diesel engine Energy 2016, 107, 305 10.1016/j.energy.2016.04.030
56. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 1985, 107, 3902 10.1021/ja00299a024
57. 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 10.1021/ct100326h
58. Rauhut, G.; Pulay, P. Transferable Scaling Factors for Density Functional Derived Vibrational Force Fields J. Phys. Chem. 1995, 99, 3093 10.1021/j100010a019
59. Pratt, L. M.; Truhlar, D. G.; Cramer, C. J.; Kass, S. R.; Thompson, J. D.; Xidos, J. D. Aggregation of Alkyllithiums in Tetrahydrofuran J. Org. Chem. 2007, 72, 2962 10.1021/jo062557o
60. Zhao, Y.; Truhlar, D. G. Computational characterization and modeling of buckyball tweezers: density functional study of concave-convex 'Ç···'Ç interactions Phys. Chem. Chem. Phys. 2008, 10, 2813 10.1039/b717744e
61. Ribeiro, R. F.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation J. Phys. Chem. B 2011, 115, 14556 10.1021/jp205508z
62. Kilpatrick, J. E.; Pitzer, K. S. Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation. III. Compound Rotation J. Chem. Phys. 1949, 17, 1064 10.1063/1.1747114
63. Pitzer, K. S. Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation: II. Unsymmetrical Tops Attached to a Rigid Frame J. Chem. Phys. 1946, 14, 239 10.1063/1.1932193
64. Pitzer, K. S.; Gwinn, W. D. Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation I. Rigid Frame with Attached Tops J. Chem. Phys. 1942, 10, 428 10.1063/1.1723744
65. Wilson, E. B., Jr.; Decius, J. C.; Cross, P. C. Molecular Vibrations; McGraw-Hill: New York, 1955; pp 54-76.
66. Jalan, A.; Alecu, I.; Meana-Pañâeda, R.; Aguilera, J.; Yang, K.; Merchant, S.; Truhlar, D. G.; Green, W. New Pathways for Formation of Acids and Carbonyl Products in Low-Temperature Oxidation: The Korcek Decomposition of η-Ketohydroperoxides J. Am. Chem. Soc. 2013, 135, 11100-11114 10.1021/ja4034439
67. Ranzi, E.; Cavallotti, C.; Cuoci, A.; Frassoldati, A.; Pelucchi, M.; Faravelli, T. New reaction classes in the kinetic modeling of low temperature oxidation of n-Alkanes Combust. Flame 2015, 162, 1679 10.1016/j.combustflame.2014.11.030
68. Zheng, J.; Zhao, Y.; Truhlar, D. G. Representative Benchmark Suites for Barrier Heights of Diverse Reaction Types and Assessment of Electronic Structure Methods for Thermochemical Kinetics J. Chem. Theory Comput. 2007, 3, 569 10.1021/ct600281g
69. Lynch, B. J.; Truhlar, D. G. Small Representative Benchmarks for Thermochemical Calculations J. Phys. Chem. A 2003, 107, 8996 10.1021/jp035287b
70. Zheng, J.; Zhao, Y.; Truhlar, D. G. The DBH24/08 Database and Its Use to Assess Electronic Structure Model Chemistries for Chemical Reaction Barrier Heights J. Chem. Theory Comput. 2009, 5, 808 10.1021/ct800568m
71. Stewart, J. J. P. Optimization of parameters for semiempirical methods I. Method J. Comput. Chem. 1989, 10, 209 10.1002/jcc.540100208
72. 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 10.1007/s00894-007-0233-4
73. Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I J. Comput. Chem. 2006, 27, 1101 10.1002/jcc.20425
74. 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 10.1063/1.3382344
75. 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 10.1007/s00894-012-1667-x
76. Stewart, J. J. P. MOPAC2016; Stewart Computational Chemistry: Colorado Springs, CO, USA. http://OpenMOPAC.net/ (accessed Dec 20, 2016).
77. Lynch, B. J.; Zhao, Y.; Truhlar, D. G. Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory J. Phys. Chem. A 2003, 107, 1384 10.1021/jp021590l
78. 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 C.01; Gaussian, Inc.: Wallingford, CT, 2010.
79. Zhao, Y.; Peverati, R.; Yang, K.; He, X.; Yu, H.; Truhlar, D. G. MNGFM, version 6.6 (computer program module); University of Minnesota: Minneapolis, MN, 2015.
80. Zheng, J.; Mielke, S. L.; Bao, J. L.; Meana-Pañâeda, R.; Clarkson, K. L.; Truhlar, D. G. MSTor-version 2017; University of Minnesota: Minneapolis, MN, 2017. https://t1.chem.umn.edu/mstor/update.htm (accessed May 5, 2017).
81. Řezáč, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods J. Chem. Theory Comput. 2012, 8, 141 10.1021/ct200751e