Dynamic QM/MM: A hybrid approach to simulating gas-liquid interactions

Topics in Current Chemistry

Volumn 307, Issue , 2012, Pages 43-68

  Yockel, Scott ^a   Schatz, George C ^b  

^a UNIVERSITY OF NORTH TEXAS   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Gas liquid scattering; Hybrid QM MM molecular dynamics; Interfacial chemistry; Room temperature ionic liquids; Squalane

Indexed keywords

DRUG DERIVATIVE; FLUORINE; IONIC LIQUID; SQUALANE; SQUALENE;

ARTICLE; BIOMECHANICS; CHEMICAL MODEL; CHEMISTRY; CONFORMATION; GAS; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; QUANTUM THEORY; SURFACE PROPERTY; THERMODYNAMICS;

BIOMECHANICS; CHEMISTRY, PHYSICAL; FLUORINE; GASES; IONIC LIQUIDS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; QUANTUM THEORY; SQUALENE; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 81855192691     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2011_130     Document Type: Article

References (52)

1. Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142-151
2. Shaik S, Cohen S, Wang Y, Chen H, Kumar D, ThielW(2010) P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. Chem Rev 110:949-1017
3. Higashi M, Truhlar DG (2008) Electrostatically embedded multiconfiguration molecular mechanics based on the combined density functional and molecular mechanical method. J Chem Theory Comput 4:790-803
4. Kamerlin SCL, Haranczyk M, Warshel A (2009) Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pK(a), redox reactions and solvation free energies. J Phys Chem B 113:1253-1272
5. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem 48:1198-1229
6. Cui Q, Karplus M (2000) Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules. J Phys Chem B 104:3721-3743
7. Cui Q, Karplus M (2000) Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. J Chem Phys 112:1133-1149
8. Gao JL, Truhlar DG (2002) Quantum mechanical methods for enzyme kinetics. Annu Rev Phys Chem 53:467-505
9. Konig PH, Hoffmann M, Frauenheim T, Cui Q (2005) A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B 109:9082-9095 (Pubitemid 40750945)
10. Lin H, Truhlar DG (2005) Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 109:3991-4004 (Pubitemid 40680414)
11. Riccardi D, Schaefer P, Cui Q (2005) pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B 109:17715-17733 (Pubitemid 41396223)
12. Shurki A, Warshel A (2003) Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. In: Adv Protein Chem 66:249-313 (Pubitemid 37392318)
13. Bakowies D, Thiel W (1996) Hybrid models for combined quantum mechanical and molecular mechanical approaches. J Phys Chem 100:10580-10594 (Pubitemid 126788646)
14. Slavicek P, Martinez TJ (2006) Multicentered valence electron effective potentials: a solution to the link atom problem for ground and excited electronic states. J Chem Phys 124:084107
15. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K (1996) ONIOM: a multilayered integrated MO \+ MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3))(2) \+ H-2 oxidative addition. J Phys Chem 100:19357-19363 (Pubitemid 126786970)
16. Vreven T, Morokuma K (2000) On the application of the IMOMO (integrated molecular orbital plus molecular orbital) method. J Comp Chem 21:1419-1432
17. Shoemaker JR, Burggraf LW, Gordon MS (1999) SIMOMM: an integrated molecular orbital/molecular mechanics optimization scheme for surfaces. J Phys Chem A 103:3245-3251
18. Rode B, Hofer TS, Randold BR, Schwenk CF, Xenides D, Vchirawongkwin V (2006) Ab initio quantum mechanical charge field (qmcf) molecular dynamics: a QM/MM-MD procedure for accurate simulations of ions and complexes. Theor Chem Acc 115:77-85 (Pubitemid 43346551)
19. Lin H, Truhlar DG (2007) QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc 117:185-199
20. Rappe AK, Goddard WA III (1991) Charge equilibration for molecular dynamics simulations. J Phys Chem 95:3358-3363
21. Heyden A, Truhlar DG (2007) Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. J Phys Chem A 111:2231-2241 (Pubitemid 46447556)
22. Rohrig UF, Frank I, Hutter J, Laio A, VandeVondele J, Rothlisberger U (2003) QM/MM carparrinello molecular dynamics study of the solvent effects on the ground stateand on the first excited singlet state of acetone in water. ChemPhysChem 4:1177-1182
23. Kerdcharoen T, Morokuma K (2002) ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase. Chem Phys Lett 355:257-263
24. Bolten K, Hase WL, Doubleday C Jr (1999) A QM/MM direct dynamics trajectory investigation of trimethlene decomposition in an argon bath. J Phys Chem B 103:3691-3698 (Pubitemid 129702421)
25. Stanton CL, Kuo I-FW, Munday CJ, Laino T, Houk KN (2007) QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-50-monophosphage decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis. J Phys Chem B 111:12573-12581 (Pubitemid 350097606)
26. Kerdcharoen T, Liedl KR, Rode BM (1996) A QM/MM simulation method applied to the solution of Li\+ in liquid ammonia. Chem Phys 211:313-323 (Pubitemid 126316522)
27. Troya D, Schatz GC (2004) Hyperthermal chemistry in the gas phase and on surfaces: theoretical studies. Int Rev Phys Chem 23:341-373 (Pubitemid 40065023)
28. Kim D, Schatz GC (2007) Theoretical investigation of hyperthermal reactions at the gasliquid interface: O (3P) and squalane. J Phys Chem A 111:5019-5031 (Pubitemid 47012614)
29. Radak B, Yockel S, Kim D, Schatz GC (2008) Modeling reactive scattering of F(2P) at a liquid squalane interface: a hybrid QM/MM molecular dynamics study. J Phys Chem A 113:7218-7226
30. Garton DJ, Minton TK, Alagia M, Balucani N, Casavecchia P, Gualberto Volpi G (2000) Comparative dynamics of Cl(2P) and O(3P) interactions with a hydrocarbon surface. J Chem Phys 112:5975-5984
31. Zhang J, Garton DJ, Minton TK (2002) Reactive and inelastic scattering dynamics of hyperthermal oxygen atoms on a saturated hydrocarbon surface. J Chem Phys 117:6239-6251 (Pubitemid 35295590)
32. Zhang J, Upadhyaya HP, Brunsvold AL, Minton TK (2006) Hyperthermal reactions of O and O2 with a hydrocarbon surface: direct C-C bond breakage by O and H-atom abstraction by O2. J Phys Chem B 110:12500-12511 (Pubitemid 44139437)
33. Perkins BG Jr, Nesbitt DJ (2006) Quantum-state-resolved CO2 scattering dynamics at the gas-liquid interface: incident collision energy and liquid dependence. J Phys Chem B 110:17126-17137 (Pubitemid 44412339)
34. Zolot AM, Harper WW, Perkins BG, Dagdigian PJ, Nesbitt DJ (2006) Quantum-state resolved reaction dynamics at the gas-liquid interface: direct absorption detection of HF(v, J) product from F(2P) \+ squalane. J Chem Phys 125:021101/1-021101/4
35. Zolot AM, Dagdigian PJ, Nesbitt DJ (2008) Quantum-state resolved reactive scattering at the gas-liquid interface: F \+ squalane (C30H62) dynamics via high-resolution infrared absorption of nascent HF(v, J). J Chem Phys 129:194705/1-194705/11
36. Wu BH, Zhang JM, Minton TK et al (2010) Scattering dynamics of hyperthermal oxygen atoms on ionic liquid surfaces: emim NTf2 and C(12)mim NTf2. J Phys Chem C 114: 4015-4027
37. Yockel S, Schatz GC (2010) Modeling O(3P) and Ar scattering from the ionic liquid [emim] [NO3] at 5 eV with hybrid QM/MM molecular dynamics. J Phys Chem B 114:14241-14248
38. Krebs T, Nathanson GM (2010) Reactive collisions of sulfur dioxide with molten carbonates. PNAS 107:6622-6627
39. Muenter AH, DeZwaan JL, Nathanson GM (2007) Interfacial interactions of DO with salty glycerol solutions of KI, NaI, LiI, and NaBr. J Phys Chem C 111:15043-15052 (Pubitemid 350068886)
40. Waring C, Bagot PAJ, Slattery JM, Costen ML, McKendrick KG (2010) O(P-3) atoms as a probe of surface ordering in 1-alkyl-3-methylimidazolium-based ionic liquids. J Phys Chem Lett 1:429-433
41. Waring C, Bagot PAJ, Slattery JM, Costen ML, McKendrick KG (2010) O(P-3) atoms as a chemical probe of surface ordering in ionic liquids. J Phys Chem A 114:4896-4904
42. Jay William Ponder (2010) TINKER-software tools for molecular design. Accessed at http://dasher.wustl.edu/tinker/
43. Bredow T, Geudtner G, Jug K (2006) MSINDO (version 3.2)
44. Ahlswede B, Jug K (1999) Consistent modifications of SINDO1: I. approximations and parameters. J Comp Chem 20:563-571 (Pubitemid 129651773)
45. Ahlswede B, Jug K (1999) Consistent modifications of SINDO1: II. Applications to first and second row elements. J Comp Chem 20:572-578 (Pubitemid 129651774)
46. Kerdcharoen T, Rodes BM (2000) What is the solvation number of Na \+ in ammonia? An ab initio QM/MM molecular dynamics study. J Phys Chem A 104:7073-7078
47. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236 (Pubitemid 26399746)
48. Bowman JM, Kuppermann A (1971) Classical and quantum reaction probabilities and thermal rate constants for the collinear H \+ H2 exchange reaction with vibrational excitation. Chem Phys Lett 12:1-4
49. Porter RN, Raff LM, Miller WH (1975) Quasiclassical selection of initial coordinates and momenta for a rotating morse oscillator. J Chem Phys 63:2214-2218
50. Canongia Lopes JN, Deschamps J, Padua AAH (2004) Modelling ionic liquids using a systematic all-atom force field. J Phys Chem B 108:2038-2047
51. Jug K, Chiodo S, Calaminici P, Avramopoulos A, Papadopoulos MG (2003) Electronic and vibrational polarizabilities and hyperpolarizabilities of azoles: a comparative study of the structure polarization relationship. J Phys Chem A 107:4172-4183
52. Raabe G, Wang Y, Fleischhauer J (2000) Calculation of the proton affinities of primary, secondary, and tertiary amines using semiempirical and ab initio methods. Z Naturforsch A 55:687-694