Ab initio transition state searching in complex systems: Fatty acid decarboxylation in minerals

Journal of Physical Chemistry A

Volumn 115, Issue 12, 2011, Pages 2658-2667

  Geatches, Dawn L ^a   Greenwell, H Christopher ^a,b   Clark, Stewart J ^a  

^a DURHAM UNIVERSITY   (United Kingdom)

^b Laboratoire de Chimie Physique et Microbiologie pour l'Environnement   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; BIOFUEL PRODUCTION; BULK SURFACES; COMPLEX SYSTEMS; DECARBOXYLATION REACTIONS; DENSITY FUNCTIONALS; FRONTIER ORBITALS; MODEL STUDY; OIL FORMATION; ORBITAL OCCUPANCY; ORGANIC SYSTEMS; PERIODIC CELL; PHYLLOSILICATE; PLANE WAVE; PROPIONIC ACIDS; TOTAL ENERGY DIFFERENCES; TRANSITION STATE; VIBRATIONAL ANALYSIS; VIBRATIONAL FREQUENCIES;

CARBON DIOXIDE; CARBOXYLATION; CATALYSIS; COMPUTATION THEORY; CRUDE OIL; DENSITY FUNCTIONAL THEORY; PARAFFINS;

FATTY ACIDS;

ALUMINUM SILICATE; FATTY ACID; MINERAL;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; CLAY; CONFORMATION; DECARBOXYLATION; QUANTUM THEORY; VIBRATION;

ALUMINUM SILICATES; CATALYSIS; DECARBOXYLATION; FATTY ACIDS; MINERALS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; QUANTUM THEORY; VIBRATION;

EID: 79953066809     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp200106x     Document Type: Article

References (48)

1. Boulet, P.; Greenwell, H. C.; Stackhouse, S.; Coveney, P. V. Recent advances in understanding the structure and reactivity of clays using electronic structure calculations J. Mol. Struct. (THEOCHEM) 2005, 762, 33-48
2. Kloprogge, J. T. Synthesis of smectites and porous pillared clay catalysts: A Review J. Porous Mater. 1998, 5, 5-41
3. Greenwell, H. C.; Jones, W.; Coveney, P. V.; Stackhouse, S. On the application of computer simulation techniques to anionic and cationic clays: A materials chemistry perspective J. Mater. Chem. 2006, 16, 708-723 (Pubitemid 43255787)
4. Almon, W. R.; Johns, W. D. Petroleum forming reactions: the mechanism and rate of clay catalyzed fatty acid decarboxilation Adv. Org. Geochem., Proc. Int. Meet. 7th 1975, 7, 157-171
5. Geatches, D. L.; Clark, S. J.; Greenwell, H. C. Role of clay minerals in oil-forming reactions J. Phys. Chem. A 2010, 114, 3569-3575
6. Prat-Resina, X.; González-Lafont, A.; Lluch, J. M. How important is the refinement of transition state structures in enzymatic reactions? J. Mol. Struct. (THEOCHEM) 2003, 632, 297-307
7. Gao, J.; Truhlar, D. Quantum mechanical methods for enzyme kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-507
8. Raab, M.; Kozmon, S.; Tvaroska, I. Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior Carbohydr. Res. 2005, 340, 1051-1057 (Pubitemid 40380834)
9. 3 (HFC-263fb) between 200 and 400 K: Ab Initio, DFT, and transition state theory calculations J. Comput. Chem. 2010, 31, 500-509
10. Simons, J.; Jørgensen, P.; Taylor, H.; Ozment, J. Walking on Potential Energy Surfaces J. Phys. Chem. 1983, 87, 2745-2753
11. Elber, R; Karplus, M. A method for determining reaction paths in large molecules-application to myoglobin Chem. Phys. Lett. 1987, 139, 375-380
12. E, W. N.; Ren, W. Q.; Vanden-Eijnden, E. String method for the study of rare events Phys. Rev. B 2002, 66, 052301-4
13. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition path sampling and the calculation of rate constants J. Chem. Phys. 1997, 108, 1964-1977
14. Koslover, E. S.; Wales, D. J. Comparison of double-ended transition state search methods J. Chem. Phys. 2007, 127, 134102-12
15. Sinclair, J. E.; Fletcher, R. A new method of saddle-point location for the calculation of defect migration energies J. Phys. C: Solid State Phys. 1974, 7, 864-870
16. Pokidova, T. S.; Denisov, E. T.; Shestakov, A. F. Kinetic parameters and geometry of the transition state of decarboxylation reactions of carboxyl and formyl radicals Pet. Chem. 2008, 48, 174-185
17. Kakkar, R.; Pathak, M.; Radhika, N. P. A DFT study of the structures of pyruvic acid isomers and their decarboxylation Org. Biomol. Chem. 2006, 4, 886-895 (Pubitemid 43289799)
18. Li, J.; Brill, T. B. Spectroscopy of hydrothermal reactions 20: experimental and DFT computational comparison of decarboxylation of dicarboxylic acids connected by single, double, and triple bonds J. Phys. Chem. A 2002, 106, 9491-9498 (Pubitemid 35410197)
19. Tietze, L. F.; Kinzel, T.; Schmatz, S. Determination of the origin of stereoselectivity in multiple-transition-state reactions using DFT calculations: enantioselective synthesis of homoallylic alcohols from aliphatic methyl ketones via an auxiliary-mediated allylation J. Am. Chem. Soc. 2008, 130, 4386-4395 (Pubitemid 351466434)
20. Yang, T.; Wen, X. D.; Li, J. F.; Yang, L. M. Theoretical and experimental investigations on the structures of purified clay and acid-activated clay Appl. Surf. Sci. 2006, 252 (18) 6154-6161 (Pubitemid 44093066)
21. Meheut, M.; Lazzeri, M.; Balan, E.; Mauri, F. Equilibrium isotopic fractionation in the kaolinite, quartz, water system: Prediction from first-principles density-functional theory Geochim. Cosmochim. Acta 2007, 71, 3170-3181 (Pubitemid 46908338)
22. Rignanese, G. M.; Gonze, X.; Pasquarello, A. First-principles study of structural, electronic, dynamical, and dielectric properties of zircon Phys. Rev. B 2001, 63, 1043051-1043057 (Pubitemid 32734060)
23. Gonze, X.; Charlier, J.-C.; Allan, D. C.; Teter, M. P. Interatomic force constants from first principles: The case of α-quartz Phys. Rev. B 1994, 50, 13035-13038
24. Greenwell, H. C.; Stackhouse, S.; Coveney, P. V.; Jones, W. A Density functional theory study of catalytic trans -esterification by tert -butoxide MgAl anionic clays J. Phys. Chem. B 2003, 107, 3476-3485
25. Breger, I. A. Diagenesis of metabolites and a discussion of the origin of petroleum hydrocarbons Geochim. Cosmochim. Acta 1960, 19, 297-308
26. Kalnes, T.; Marker, T.; Shonnard, D. R. Green diesel: A second generation biofuel Int. J. Chem. React. Eng. 2007, 5, A48
27. Wyckoff, R. W. G. Crystal Structures; John Wiley and Sons: Chichester, 1968.
28. Larentzos, J. P.; Greathouse, J. A.; Cygan, R. T. An ab initio and classical molecular dynamics investigation of the structural and vibrational properties of talc and pyrophillite J. Phys. Chem. C 2007, 111 (34) 12752-12759 (Pubitemid 47388109)
29. Clark, S. J.; Segall, M. D.; Pickard, C. J.; Hasnip, P. J.; Probert, M. J.; Refson, K.; Payne, M. C. Z. Kristallogr. 2005, 220 (5) 567-570
30. Kohn, W.; Sham, L. J. Self-consistent equations including exchange and correlation effects Phys. Rev. 1965, 140 (4A) A1133-A1138
31. Kohn, W.; Sham, L. J. Quantum density oscillations in an inhomogeneous electron gas J. Phys. Rev. 1965, 137 (6A) A1697-A1705
32. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple Phys. Rev. Lett. 1996, 77 (18) 3865-3868 (Pubitemid 126631804)
33. Kurth, S.; Perdew, J. P.; Blaha, P. Molecular and solid state tests of density functional approximations: LSD, GGAs, and meta-GGAs Int. J. Quantum Chem. 1999, 75, 889-909 (Pubitemid 129648121)
34. Vanderbilt, D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism Phys. Rev. B 1990, 41 (11) 7892-7895
35. Mazari, N.; Vanderbilt, D.; Payne, M. C. Ensemble density functional theory for ab initio molecular dynamics of metals and finite-temperature insulators Phys. Rev. Lett. 1997, 79 (7) 1337-1340 (Pubitemid 127658427)
36. Govind, N.; Petersen, M.; Fitzgerald, G.; King-Smith, D.; Andzelm, J. A generalized synchronous transit method for transition state location Comput. Mater. Sci. 2003, 28, 250-258
37. Gonze, X. First-principles responses of solids to atomic displacements and homogeneous electric fields: Implementation of a conjugate-gradient algorithm Phys. Rev. B 1997, 55, 10337-10354
38. Lin, J. S.; Qteish, A.; Payne, M. C.; Heine, V. Optimized and transfereable nonlocal separable ab initio pseudopotentials Phys. Rev. B 1993, 47, 4174-4180
39. Teter, M. P.; Payne, M. C.; Allan, D. C. Solution of Schrödinger's equation for large systems Phys. Rev. B 1989, 40, 12255-12263
40. Zhang, A.; Ma, Q.; Wang, K.; Tang, Y.; Goddard, W. A. Improved processes to remove naphthenic acids. Final Technical Report DE-FC26-02NT15383, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, 2005.
41. 3 catalysts Catal. Today 2005, 100, 331-335
42. Fukui, K. The path of chemical reactions-the IRC approach Acc. Chem. Res. 1981, 14, 363-368
43. Kraka, E.; Cremer, D. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: Hidden intermediates and hidden transition states Acc. Chem. Res. 2010, 43, 591-601
44. Farmer, V. C. The Infrared Spectra of Minerals; Mineralogical Society: London, 1974.
45. Sainz-Diaz, C. L.; Escamilla-Roa, E.; Hernandez-Laguna, A. Pyrophyllite dehydroxylation process by first principles calculations Am. Mineral. 2004, 89, 1092-1100 (Pubitemid 39058451)
46. Mulliken, R. S. Electronic population analysis on LCAO-MO molecular wavefunctions * 1 J. Chem. Phys. 1955, 23 (10) 1833-1840
47. Suter, J. L.; Anderson, R. L.; Greenwell, H. C.; Coveney, P. V. Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals J. Mater. Chem 2009, 19, 2482-2493
48. Smith, B.; Greenwell, H. C.; Whiting, A. Catalytic upgrading of tri-glycerides and fatty acids to transport biofuels Energy Environ. Sci. 2009, 2, 262-271