메뉴 건너뛰기




Volumn 120, Issue 2, 2016, Pages 299-305

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; CALCULATIONS; CHEMICAL REACTIONS; FREE ENERGY; MOLECULAR DYNAMICS; POTENTIAL ENERGY; QUANTUM CHEMISTRY; REACTION KINETICS; SURFACE REACTIONS;

EID: 84955517278     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/acs.jpca.5b10667     Document Type: Article
Times cited : (54)

References (33)
  • 1
    • 84892738066 scopus 로고    scopus 로고
    • Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances
    • Klippenstein, S. J.; Pande, V. S.; Truhlar, D. G. Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances J. Am. Chem. Soc. 2014, 136, 528-546 10.1021/ja408723a
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 528-546
    • Klippenstein, S.J.1    Pande, V.S.2    Truhlar, D.G.3
  • 4
    • 84902817448 scopus 로고    scopus 로고
    • Well-Tempered Metadynamics Converges Asymptotically
    • Dama, J. F.; Parrinello, M.; Voth, G. A. Well-Tempered Metadynamics Converges Asymptotically Phys. Rev. Lett. 2014, 112, 240602 10.1103/PhysRevLett.112.240602
    • (2014) Phys. Rev. Lett. , vol.112 , pp. 240602
    • Dama, J.F.1    Parrinello, M.2    Voth, G.A.3
  • 5
    • 84903938993 scopus 로고    scopus 로고
    • Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
    • Iannuzzi, M.; Laio, A.; Parrinello, M. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics Phys. Rev. Lett. 2003, 90, 238302 10.1103/PhysRevLett.90.238302
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 238302
    • Iannuzzi, M.1    Laio, A.2    Parrinello, M.3
  • 6
    • 33644968698 scopus 로고    scopus 로고
    • Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions
    • Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M. L. Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions Acc. Chem. Res. 2006, 39, 73-81 10.1021/ar040198i
    • (2006) Acc. Chem. Res. , vol.39 , pp. 73-81
    • Ensing, B.1    De Vivo, M.2    Liu, Z.3    Moore, P.4    Klein, M.L.5
  • 7
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science
    • Laio, A.; Gervasio, F. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science Rep. Prog. Phys. 2008, 71, 126601 10.1088/0034-4885/71/12/126601
    • (2008) Rep. Prog. Phys. , vol.71 , pp. 126601
    • Laio, A.1    Gervasio, F.L.2
  • 8
    • 84926210854 scopus 로고    scopus 로고
    • Enhanced Sampling of Chemical and Biochemical Reactions with Metadynamics
    • Zheng, S.; Pfaendtner, J. Enhanced Sampling of Chemical and Biochemical Reactions with Metadynamics Mol. Simul. 2015, 41, 55-72 10.1080/08927022.2014.923574
    • (2015) Mol. Simul. , vol.41 , pp. 55-72
    • Zheng, S.1    Pfaendtner, J.2
  • 9
    • 84889779905 scopus 로고    scopus 로고
    • From Metadynamics to Dynamics
    • Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics Phys. Rev. Lett. 2013, 111, 230602 10.1103/PhysRevLett.111.230602
    • (2013) Phys. Rev. Lett. , vol.111 , pp. 230602
    • Tiwary, P.1    Parrinello, M.2
  • 10
    • 84922224593 scopus 로고    scopus 로고
    • Kinetics of Protein-Ligand Unbinding: Predicting Pathways, Rates, and Rate-Limiting Steps
    • Tiwary, P.; Limongelli, V.; Salvalaglio, M.; Parrinello, M. Kinetics of Protein-Ligand Unbinding: Predicting Pathways, Rates, and Rate-Limiting Steps Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E386-E391 10.1073/pnas.1424461112
    • (2015) Proc. Natl. Acad. Sci. U. S. A. , vol.112 , pp. E386-E391
    • Tiwary, P.1    Limongelli, V.2    Salvalaglio, M.3    Parrinello, M.4
  • 11
    • 84942937974 scopus 로고    scopus 로고
    • Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding
    • Tiwary, P.; Mondal, J.; Morrone, J. A.; Berne, B. Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12015-12019 10.1073/pnas.1516652112
    • (2015) Proc. Natl. Acad. Sci. U. S. A. , vol.112 , pp. 12015-12019
    • Tiwary, P.1    Mondal, J.2    Morrone, J.A.3    Berne, B.4
  • 12
    • 84898429568 scopus 로고    scopus 로고
    • Assessing the Reliability of the Dynamics Reconstructed from Metadynamics
    • Salvalaglio, M.; Tiwary, P.; Parrinello, M. Assessing the Reliability of the Dynamics Reconstructed from Metadynamics J. Chem. Theory Comput. 2014, 10, 1420-1425 10.1021/ct500040r
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 1420-1425
    • Salvalaglio, M.1    Tiwary, P.2    Parrinello, M.3
  • 13
    • 1442281293 scopus 로고    scopus 로고
    • A Method for Accelerating the Molecular Dynamics Simulation of Infrequent Events
    • Voter, A. F. A Method for Accelerating the Molecular Dynamics Simulation of Infrequent Events J. Chem. Phys. 1997, 106, 4665-4677 10.1063/1.473503
    • (1997) J. Chem. Phys. , vol.106 , pp. 4665-4677
    • Voter, A.F.1
  • 14
    • 84944236979 scopus 로고    scopus 로고
    • Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds
    • Bal, K. M.; Neyts, E. C. Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds J. Chem. Theory Comput. 2015, 11, 4545-4554 10.1021/acs.jctc.5b00597
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 4545-4554
    • Bal, K.M.1    Neyts, E.C.2
  • 15
    • 0036424048 scopus 로고    scopus 로고
    • Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark
    • Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark Annu. Rev. Phys. Chem. 2002, 53, 291-318 10.1146/annurev.physchem.53.082301.113146
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 16
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of Parameters for Semiempirical Methods V: Modification of Nddo Approximations and Application to 70 Elements
    • Stewart, 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 10.1007/s00894-007-0233-4
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.P.1
  • 17
    • 0029633186 scopus 로고
    • Amber, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
    • Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Amber, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules Comput. Phys. Commun. 1995, 91, 1-41 10.1016/0010-4655(95)00041-D
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    DeBolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 19
    • 4243606192 scopus 로고
    • Unified Approach for Molecular Dynamics and Density-Functional Theory
    • Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory Phys. Rev. Lett. 1985, 55, 2471 10.1103/PhysRevLett.55.2471
    • (1985) Phys. Rev. Lett. , vol.55 , pp. 2471
    • Car, R.1    Parrinello, M.2
  • 20
    • 0001161603 scopus 로고
    • Efficacious Form for Model Pseudopotentials
    • Kleinman, L.; Bylander, D. Efficacious Form for Model Pseudopotentials Phys. Rev. Lett. 1982, 48, 1425 10.1103/PhysRevLett.48.1425
    • (1982) Phys. Rev. Lett. , vol.48 , pp. 1425
    • Kleinman, L.1    Bylander, D.2
  • 21
    • 4243553426 scopus 로고
    • Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior
    • Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
    • (1988) Phys. Rev. A: At., Mol., Opt. Phys. , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 22
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density
    • 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: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
    • (1988) Phys. Rev. B: Condens. Matter Mater. Phys. , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 23
    • 34547809547 scopus 로고
    • A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods
    • Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods J. Chem. Phys. 1984, 81, 511-519 10.1063/1.447334
    • (1984) J. Chem. Phys. , vol.81 , pp. 511-519
    • Nose, S.1
  • 24
    • 0001538909 scopus 로고
    • Canonical Dynamics - Equilibrium Phase-Space Distributions
    • Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697 10.1103/PhysRevA.31.1695
    • (1985) Phys. Rev. A: At., Mol., Opt. Phys. , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 26
    • 38349091489 scopus 로고    scopus 로고
    • Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
    • Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Phys. Rev. Lett. 2008, 100, 020603 10.1103/PhysRevLett.100.020603
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 020603
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 28
    • 4244179012 scopus 로고
    • Frequency Factors and Isotope Effects in Solid State Rate Processes
    • Vineyard, G. H. Frequency Factors and Isotope Effects in Solid State Rate Processes J. Phys. Chem. Solids 1957, 3, 121-127 10.1016/0022-3697(57)90059-8
    • (1957) J. Phys. Chem. Solids , vol.3 , pp. 121-127
    • Vineyard, G.H.1
  • 29
    • 84907327659 scopus 로고    scopus 로고
    • A Time-Independent Free Energy Estimator for Metadynamics
    • Tiwary, P.; Parrinello, M. A Time-Independent Free Energy Estimator for Metadynamics J. Phys. Chem. B 2015, 119, 736-742 10.1021/jp504920s
    • (2015) J. Phys. Chem. B , vol.119 , pp. 736-742
    • Tiwary, P.1    Parrinello, M.2
  • 30
    • 0030955631 scopus 로고    scopus 로고
    • A Detailed Kinetic Modeling Study of Aromatics Formation in Laminar Premixed Acetylene and Ethylene Flames
    • Wang, H.; Frenklach, M. A Detailed Kinetic Modeling Study of Aromatics Formation in Laminar Premixed Acetylene and Ethylene Flames Combust. Flame 1997, 110, 173-221 10.1016/S0010-2180(97)00068-0
    • (1997) Combust. Flame , vol.110 , pp. 173-221
    • Wang, H.1    Frenklach, M.2
  • 31
    • 84901373253 scopus 로고    scopus 로고
    • Car-Parrinello Molecular Dynamics+ Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables
    • Zheng, S.; Pfaendtner, J. Car-Parrinello Molecular Dynamics+ Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables J. Phys. Chem. C 2014, 118, 10764-10770 10.1021/jp500398k
    • (2014) J. Phys. Chem. C , vol.118 , pp. 10764-10770
    • Zheng, S.1    Pfaendtner, J.2
  • 32
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science
    • Laio, A.; Gervasio, F. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science Rep. Prog. Phys. 2008, 71, 126601 10.1088/0034-4885/71/12/126601
    • (2008) Rep. Prog. Phys. , vol.71 , pp. 126601
    • Laio, A.1    Gervasio, F.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.