메뉴 건너뛰기




Volumn 6, Issue 5, 2010, Pages 1490-1497

Dual grid methods for finding the reaction path on reduced potential energy surfaces

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77952343449     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct100012y     Document Type: Article
Times cited : (28)

References (50)
  • 2
    • 0037008011 scopus 로고    scopus 로고
    • Multiple conformational changes in enzyme catalysis
    • Hammes, G. G. Multiple conformational changes in enzyme catalysis Biochemistry 2002, 41 (26) 8221
    • (2002) Biochemistry , vol.41 , Issue.26 , pp. 8221
    • Hammes, G.G.1
  • 4
    • 36749120357 scopus 로고
    • Reaction path Hamiltonian for polyatomic molecules
    • Miller, W. H.; Handy, N. C.; Adams, J. E. Reaction Path Hamiltonian for Polyatomic Molecules J. Chem. Phys. 1980, 72 (1) 99
    • (1980) J. Chem. Phys. , vol.72 , Issue.1 , pp. 99
    • Miller, W.H.1    Handy, N.C.2    Adams, J.E.3
  • 5
    • 36549095692 scopus 로고
    • An improved algorithm for reaction path following
    • Gonzalez, C.; Schlegel, H. B. An improved algorithm for reaction path following J. Chem. Phys. 1989, 90 (4) 2154-2161
    • (1989) J. Chem. Phys. , vol.90 , Issue.4 , pp. 2154-2161
    • Gonzalez, C.1    Schlegel, H.B.2
  • 6
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena Chem. Rev. 1993, 93 (7) 2395-2417
    • (1993) Chem. Rev. , vol.93 , Issue.7 , pp. 2395-2417
    • Kollman, P.1
  • 7
    • 0035608214 scopus 로고    scopus 로고
    • Finding transition states using reduced potential-energy surfaces
    • Bofill, J. M.; Anglada, J. M. Finding transition states using reduced potential-energy surfaces Theor. Chem. Acc. 2001, 105 (6) 463-472
    • (2001) Theor. Chem. Acc. , vol.105 , Issue.6 , pp. 463-472
    • Bofill, J.M.1    Anglada, J.M.2
  • 8
    • 84986513718 scopus 로고
    • Updated Hessian matrix and the restricted step method for locating transition structures
    • Bofill, J. M. Updated Hessian matrix and the restricted step method for locating transition structures J. Comput. Chem. 1994, 15 (1) 1-11
    • (1994) J. Comput. Chem. , vol.15 , Issue.1 , pp. 1-11
    • Bofill, J.M.1
  • 9
    • 33845540187 scopus 로고
    • A quasi-Newton algorithm for first-order saddle-point location
    • Culot, P.; Dive, G.; Nguyen, V.; Ghuysen, J. A quasi-Newton algorithm for first-order saddle-point location Theor. Chim. Acta 1992, 82, 189-205
    • (1992) Theor. Chim. Acta , vol.82 , pp. 189-205
    • Culot, P.1    Dive, G.2    Nguyen, V.3    Ghuysen, J.4
  • 10
    • 0001476184 scopus 로고    scopus 로고
    • Defect migration in crystalline silicon
    • Munro, L. J.; Wales, D. J. Defect migration in crystalline silicon Phys. Rev. B 1999, 59, 3969-3980
    • (1999) Phys. Rev. B , vol.59 , pp. 3969-3980
    • Munro, L.J.1    Wales, D.J.2
  • 11
    • 0001361692 scopus 로고    scopus 로고
    • Transition states and rearrangement mechanisms from hybrid eigenvector-following and density functional theory.: Application to C10H10 and defect migration in crystalline silicon
    • Kumeda, Y.; Wales, D. J.; Munro, L. J. Transition states and rearrangement mechanisms from hybrid eigenvector-following and density functional theory.: Application to C10H10 and defect migration in crystalline silicon Chem. Phys. Lett. 2001, 341 (1) 185
    • (2001) Chem. Phys. Lett. , vol.341 , Issue.1 , pp. 185
    • Kumeda, Y.1    Wales, D.J.2    Munro, L.J.3
  • 13
    • 0000327364 scopus 로고    scopus 로고
    • A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
    • Henkelman, G.; Jónsson, H. A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives J. Chem. Phys. 1999, 111, 7010
    • (1999) J. Chem. Phys. , vol.111 , pp. 7010
    • Henkelman, G.1    Jónsson, H.2
  • 14
    • 77952347763 scopus 로고    scopus 로고
    • Methods for finding transition states on reduced potential energy surfaces
    • accepted)
    • Burger, S. K.; Ayers, P. W., Methods for finding transition states on reduced potential energy surfaces. J. Chem. Phys. 2010, (accepted).
    • (2010) J. Chem. Phys.
    • Burger, S.K.1    Ayers, P.W.2
  • 15
    • 34247881948 scopus 로고    scopus 로고
    • Simplified and improved string method for computing the minimum energy paths in barrier-crossing events
    • E, W. N.; Ren, W. Q.; Vanden-Eijnden, E. Simplified and improved string method for computing the minimum energy paths in barrier-crossing events J. Chem. Phys. 2007, 126 (16) 164103
    • (2007) J. Chem. Phys. , vol.126 , Issue.16 , pp. 164103
    • E, W.N.1    Ren, W.Q.2    Vanden-Eijnden, E.3
  • 16
    • 0036696910 scopus 로고    scopus 로고
    • String method for the study of rare events
    • 052301
    • E, W. N.; Ren, W. Q.; Vanden-Eijnden, E. String method for the study of rare events Phys. Rev. B 2002, 66 (5 052301
    • (2002) Phys. Rev. B , vol.66 , Issue.5
    • E, W.N.1    Ren, W.Q.2    Vanden-Eijnden, E.3
  • 17
    • 1242329035 scopus 로고    scopus 로고
    • Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
    • DOI 10.1063/1.1323224
    • Henkelman, G.; Jonsson, H. Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 2000, 113 (22) 9978-9985 (Pubitemid 32076892)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.22 , pp. 9978-9985
    • Henkelman, G.1    Jonsson, H.2
  • 18
    • 0034513054 scopus 로고    scopus 로고
    • Climbing image nudged elastic band method for finding saddle points and minimum energy paths
    • DOI 10.1063/1.1329672
    • Henkelman, G.; Uberuaga, B. P.; Jonsson, H. A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 2000, 113 (22) 9901-9904 (Pubitemid 32076883)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.22 , pp. 9901-9904
    • Henkelman, G.1    Uberuaga, B.P.2    Jonsson, H.3
  • 19
    • 33746255471 scopus 로고    scopus 로고
    • String method in collective variables: Minimum free energy paths and isocommittor surfaces
    • 024106
    • Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String method in collective variables: Minimum free energy paths and isocommittor surfaces J. Chem. Phys. 2006, 125 (2 024106
    • (2006) J. Chem. Phys. , vol.125 , Issue.2
    • Maragliano, L.1    Fischer, A.2    Vanden-Eijnden, E.3    Ciccotti, G.4
  • 20
    • 2442486484 scopus 로고    scopus 로고
    • A growing string method for determining transition states: Comparison to the nudged elastic band and string methods
    • Peters, B.; Heyden, A.; Bell, A. T. A growing string method for determining transition states: Comparison to the nudged elastic band and string methods J. Chem. Phys. 2004, 120 (17) 7877-7886
    • (2004) J. Chem. Phys. , vol.120 , Issue.17 , pp. 7877-7886
    • Peters, B.1    Heyden, A.2    Bell, A.T.3
  • 21
    • 18744412161 scopus 로고    scopus 로고
    • A growing string method for the reaction pathway defined by a Newton trajectory
    • Quapp, W. A growing string method for the reaction pathway defined by a Newton trajectory J. Chem. Phys. 2005, 122 (17) 174106
    • (2005) J. Chem. Phys. , vol.122 , Issue.17 , pp. 174106
    • Quapp, W.1
  • 22
    • 3042596593 scopus 로고    scopus 로고
    • Reaction pathways and projection operators: Application to string methods
    • Quapp, W. Reaction pathways and projection operators: Application to string methods J. Comput. Chem. 2004, 25 (10) 1277-1285
    • (2004) J. Comput. Chem. , vol.25 , Issue.10 , pp. 1277-1285
    • Quapp, W.1
  • 23
    • 36048930097 scopus 로고    scopus 로고
    • Sequential quadratic programming method for determining the minimum energy path
    • Burger, S. K.; Yang, W. T. Sequential quadratic programming method for determining the minimum energy path J. Chem. Phys. 2007, 127 (16) 164107
    • (2007) J. Chem. Phys. , vol.127 , Issue.16 , pp. 164107
    • Burger, S.K.1    Yang, W.T.2
  • 24
    • 33745160122 scopus 로고    scopus 로고
    • Quadratic string method for determining the minimum-energy path based on multiobjective optimization
    • 054109
    • Burger, S. K.; Yang, W. T. Quadratic string method for determining the minimum-energy path based on multiobjective optimization J. Chem. Phys. 2006, 124 (5 054109
    • (2006) J. Chem. Phys. , vol.124 , Issue.5
    • Burger, S.K.1    Yang, W.T.2
  • 25
    • 0000118540 scopus 로고    scopus 로고
    • A combined method for determining reaction paths, minima, and transition state geometries
    • Ayala, P. Y.; Schlegel, H. B. A combined method for determining reaction paths, minima, and transition state geometries J. Chem. Phys. 1997, 107 (2) 375-384
    • (1997) J. Chem. Phys. , vol.107 , Issue.2 , pp. 375-384
    • Ayala, P.Y.1    Schlegel, H.B.2
  • 26
    • 36449003859 scopus 로고
    • Locating transition structures by mode following: A comparison of six methods on the Ar8 Lennard-Jones potential
    • Jensen, F. Locating transition structures by mode following: A comparison of six methods on the Ar8 Lennard-Jones potential J. Chem. Phys. 1995, 102, 6706
    • (1995) J. Chem. Phys. , vol.102 , pp. 6706
    • Jensen, F.1
  • 27
    • 2442481958 scopus 로고    scopus 로고
    • Using redundant internal coordinates to optimize equilibrium geometries and transition states
    • Peng, C.; Ayala, P.; Schlegel, H.; Frisch, M. Using redundant internal coordinates to optimize equilibrium geometries and transition states J. Comput. Chem. 1996, 17 (1) 49-56
    • (1996) J. Comput. Chem. , vol.17 , Issue.1 , pp. 49-56
    • Peng, C.1    Ayala, P.2    Schlegel, H.3    Frisch, M.4
  • 28
    • 34548083705 scopus 로고    scopus 로고
    • Geometry optimization using generalized, chemically meaningful constraints
    • Budzelaar, P. Geometry optimization using generalized, chemically meaningful constraints J. Comput. Chem. 2007, 28 (13) 2226-2236
    • (2007) J. Comput. Chem. , vol.28 , Issue.13 , pp. 2226-2236
    • Budzelaar, P.1
  • 29
    • 36449006558 scopus 로고
    • Molecular-potential energy surfaces by interpolation
    • Ischtwan, J.; Collins, M. A. Molecular-Potential Energy Surfaces by Interpolation J. Chem. Phys. 1994, 100 (11) 8080-8088
    • (1994) J. Chem. Phys. , vol.100 , Issue.11 , pp. 8080-8088
    • Ischtwan, J.1    Collins, M.A.2
  • 30
    • 0036882785 scopus 로고    scopus 로고
    • Molecular potential-energy surfaces for chemical reaction dynamics
    • Collins, M. A. Molecular potential-energy surfaces for chemical reaction dynamics Theor. Chem. Acc. 2002, 108 (6) 313-324
    • (2002) Theor. Chem. Acc. , vol.108 , Issue.6 , pp. 313-324
    • Collins, M.A.1
  • 31
    • 58649123095 scopus 로고    scopus 로고
    • Moving least-squares enhanced Shepard interpolation for the fast marching and string methods
    • 024103
    • Burger, S. K.; Liu, Y.; Sarkar, U.; Ayers, P. W. Moving least-squares enhanced Shepard interpolation for the fast marching and string methods J. Chem. Phys. 2009, 130 024103
    • (2009) J. Chem. Phys. , vol.130
    • Burger, S.K.1    Liu, Y.2    Sarkar, U.3    Ayers, P.W.4
  • 32
    • 34248376539 scopus 로고    scopus 로고
    • Interpolating moving least-squares methods for fitting potential energy surfaces: Computing high-density potential energy surface data from low-density ab initio data points
    • 084107
    • Dawes, R.; Thompson, D. L.; Guo, Y.; Wagner, A. F.; Minkoff, M. Interpolating moving least-squares methods for fitting potential energy surfaces: Computing high-density potential energy surface data from low-density ab initio data points J. Chem. Phys. 2007, 126 (18 084107
    • (2007) J. Chem. Phys. , vol.126 , Issue.18
    • Dawes, R.1    Thompson, D.L.2    Guo, Y.3    Wagner, A.F.4    Minkoff, M.5
  • 33
    • 2342455212 scopus 로고    scopus 로고
    • Improving the accuracy of interpolated potential energy surfaces by using an analytical zeroth-order potential function
    • Kawano, A.; Guo, Y.; Thompson, D. L.; Wagner, A. F.; Minkoff, M. Improving the accuracy of interpolated potential energy surfaces by using an analytical zeroth-order potential function J. Chem. Phys. 2004, 120 (14) 6414-6422
    • (2004) J. Chem. Phys. , vol.120 , Issue.14 , pp. 6414-6422
    • Kawano, A.1    Guo, Y.2    Thompson, D.L.3    Wagner, A.F.4    Minkoff, M.5
  • 34
    • 33847283956 scopus 로고    scopus 로고
    • Computing tunneling paths with the Hamilton-Jacobi equation and the fast marching method
    • Dey, B. K.; Ayers, P. W. Computing tunneling paths with the Hamilton-Jacobi equation and the fast marching method Mol. Phys. 2007, 105 (1) 71-83
    • (2007) Mol. Phys. , vol.105 , Issue.1 , pp. 71-83
    • Dey, B.K.1    Ayers, P.W.2
  • 35
    • 32444448669 scopus 로고    scopus 로고
    • A Hamilton-Jacobi type equation for computing minimum potential energy paths
    • Dey, B. K.; Ayers, P. W. A Hamilton-Jacobi type equation for computing minimum potential energy paths Mol. Phys. 2006, 104 (4) 541-558
    • (2006) Mol. Phys. , vol.104 , Issue.4 , pp. 541-558
    • Dey, B.K.1    Ayers, P.W.2
  • 36
    • 33846423590 scopus 로고    scopus 로고
    • Fast marching method for calculating reactive trajectories for chemical reactions
    • Dey, B. K.; Bothwell, S.; Ayers, P. W. Fast marching method for calculating reactive trajectories for chemical reactions J. Math. Chem. 2007, 41 (1) 1-25
    • (2007) J. Math. Chem. , vol.41 , Issue.1 , pp. 1-25
    • Dey, B.K.1    Bothwell, S.2    Ayers, P.W.3
  • 37
    • 7544228185 scopus 로고    scopus 로고
    • Hamilton-Jacobi equation for the least-action/least-time dynamical path based on fast marching method
    • Dey, B. K.; Janicki, M. R.; Ayers, P. W. Hamilton-Jacobi equation for the least-action/least-time dynamical path based on fast marching method J. Chem. Phys. 2004, 121 (14) 6667-6679
    • (2004) J. Chem. Phys. , vol.121 , Issue.14 , pp. 6667-6679
    • Dey, B.K.1    Janicki, M.R.2    Ayers, P.W.3
  • 38
    • 22944492404 scopus 로고    scopus 로고
    • Interpolated potential energy surfaces: How accurate do the second derivatives have to be.
    • Crittenden, D. L.; Jordan, M. J. T. Interpolated potential energy surfaces: How accurate do the second derivatives have to be. J. Chem. Phys. 2005, 122 ((4).
    • (2005) J. Chem. Phys , vol.122 , Issue.4
    • Crittenden, D.L.1    Jordan, M.J.T.2
  • 39
    • 10844258426 scopus 로고    scopus 로고
    • Learning to interpolate molecular potential energy surfaces with confidence: A Bayesian approach
    • Bettens, R. P. A.; Collins, M. A. Learning to interpolate molecular potential energy surfaces with confidence: A Bayesian approach J. Chem. Phys. 1999, 111 (3) 816-826
    • (1999) J. Chem. Phys. , vol.111 , Issue.3 , pp. 816-826
    • Bettens, R.P.A.1    Collins, M.A.2
  • 40
    • 36448999897 scopus 로고
    • The utility of higher-order derivatives in constructing molecular-potential energy surfaces by interpolation
    • Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. The Utility of Higher-Order Derivatives in Constructing Molecular-Potential Energy Surfaces by Interpolation J. Chem. Phys. 1995, 103 (22) 9669-9675
    • (1995) J. Chem. Phys. , vol.103 , Issue.22 , pp. 9669-9675
    • Jordan, M.J.T.1    Thompson, K.C.2    Collins, M.A.3
  • 41
    • 0000677365 scopus 로고
    • The analytical representation of electronic potential-energy surfaces
    • Schatz, G. C. The analytical representation of electronic potential-energy surfaces Rev. Mod. Phys. 1989, 61 (3) 669-688
    • (1989) Rev. Mod. Phys. , vol.61 , Issue.3 , pp. 669-688
    • Schatz, G.C.1
  • 42
    • 84966242872 scopus 로고
    • Rate of convergence of shepard global interpolation formula
    • Farwig, R. Rate of convergence of shepard global interpolation formula Math. Comput. 1986, 46 (174) 577-590
    • (1986) Math. Comput. , vol.46 , Issue.174 , pp. 577-590
    • Farwig, R.1
  • 47
    • 56549109896 scopus 로고    scopus 로고
    • Theoretical Investigation of mono- and bi-function alkylating agents
    • Lu, C. L.; Liu, Y. D.; Zhong, R. G. Theoretical Investigation of mono- and bi-function alkylating agents J. Mol. Struct. THEOCHEM 2009, 893, 106-110
    • (2009) J. Mol. Struct. THEOCHEM , vol.893 , pp. 106-110
    • Lu, C.L.1    Liu, Y.D.2    Zhong, R.G.3
  • 49
    • 0034625082 scopus 로고    scopus 로고
    • Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects
    • Parikh, S.; Walcher, G.; Jones, G.; Slupphaug, G.; Krokan, H.; Blackburn, G.; Tainer, J. Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects Proc. Natl. Acad. Sci. 2000, 97 (10) 5083
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , Issue.10 , pp. 5083
    • Parikh, S.1    Walcher, G.2    Jones, G.3    Slupphaug, G.4    Krokan, H.5    Blackburn, G.6    Tainer, J.7
  • 50
    • 0035909316 scopus 로고    scopus 로고
    • Uracil-DNA glycosylase acts by substrate autocatalysis
    • Dinner, A. R.; Blackburn, G. M.; Karplus, M. W. Uracil-DNA glycosylase acts by substrate autocatalysis Nature 2001, 413, 752
    • (2001) Nature , vol.413 , pp. 752
    • Dinner, A.R.1    Blackburn, G.M.2    Karplus, M.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.