-
1
-
-
0017100947
-
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel A., and Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103 (1976) 227-249
-
(1976)
J Mol Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
2
-
-
21244497608
-
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
-
Compact overview of QM, MM and QM/MM methodology with detailed discussion of selected QM/MM applications to enzymatic reactions. The authors also discuss the understanding of enzyme catalysis and the performance of QM/MM models in general.
-
Friesner R.A., and Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu Rev Phys Chem 56 (2005) 389-427. Compact overview of QM, MM and QM/MM methodology with detailed discussion of selected QM/MM applications to enzymatic reactions. The authors also discuss the understanding of enzyme catalysis and the performance of QM/MM models in general.
-
(2005)
Annu Rev Phys Chem
, vol.56
, pp. 389-427
-
-
Friesner, R.A.1
Guallar, V.2
-
3
-
-
33748608826
-
Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency
-
Bruice T.C. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 106 (2006) 3119-3139
-
(2006)
Chem Rev
, vol.106
, pp. 3119-3139
-
-
Bruice, T.C.1
-
4
-
-
33646356998
-
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes
-
a calculations and proton-transport processes.
-
a calculations and proton-transport processes.
-
(2006)
J Phys Chem B
, vol.110
, pp. 6458-6469
-
-
Riccardi, D.1
Schaefer, P.2
Yang, Y.3
Yu, H.4
Ghosh, N.5
Prat-Resina, X.6
König, P.7
Li, G.8
Xu, D.9
Guo, H.10
-
5
-
-
33846570818
-
-
Lin H, Truhlar DG: QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc, Epub ahead of print, DOI:10.1007/s00214-006-0143-z. Succinct review of current methodological issues of the QM/MM approach.
-
-
-
-
6
-
-
34047178059
-
-
Senn HM, Thiel W: QM/MM methods for biological systems. In Atomistic Approaches in Modern Biology. (Topics in Current Chemistry, Vol 268). Edited by Reiher M. Berlin: Springer; 2007:173-290. Extensive review of the state of the art of the QM/MM method, including its use in optimization and simulation schemes. Tabular survey of biomolecular applications covering the period 2000 to mid-2006.
-
-
-
-
7
-
-
0346726109
-
How enzymes work: analysis by modern rate theory and computer simulations
-
Garcia-Viloca M., Gao J., Karplus M., and Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
-
(2004)
Science
, vol.303
, pp. 186-195
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
8
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
Systematic presentation of the arguments supporting the concept of electrostatic transition-state stabilization to rationalize enzyme catalysis. Alternative proposals are summarized and held against transition-state stabilization.
-
Warshel A., Sharma P.K., Kato M., Xiang Y., Liu H., and Olsson M.H.M. Electrostatic basis for enzyme catalysis. Chem Rev 106 (2006) 3210-3235. Systematic presentation of the arguments supporting the concept of electrostatic transition-state stabilization to rationalize enzyme catalysis. Alternative proposals are summarized and held against transition-state stabilization.
-
(2006)
Chem Rev
, vol.106
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.5
Olsson, M.H.M.6
-
9
-
-
19944408652
-
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method
-
König P.H., Hoffmann M., Frauenheim T., and Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B 109 (2005) 9082-9095
-
(2005)
J Phys Chem B
, vol.109
, pp. 9082-9095
-
-
König, P.H.1
Hoffmann, M.2
Frauenheim, T.3
Cui, Q.4
-
10
-
-
18844410543
-
Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations
-
Lin H., and Truhlar D.G. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 109 (2005) 3991-4004
-
(2005)
J Phys Chem A
, vol.109
, pp. 3991-4004
-
-
Lin, H.1
Truhlar, D.G.2
-
11
-
-
19944369519
-
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
-
Nam K., Gao J., and York D.M. An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations. J Chem Theory Comput 1 (2005) 2-13
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 2-13
-
-
Nam, K.1
Gao, J.2
York, D.M.3
-
12
-
-
34548059996
-
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
-
014905/1-14
-
Schaefer P., Riccardi D., and Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys 123 (2005) 014905/1-14
-
(2005)
J Chem Phys
, vol.123
-
-
Schaefer, P.1
Riccardi, D.2
Cui, Q.3
-
13
-
-
25844473576
-
a calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols
-
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 (2005) 17715-17733
-
(2005)
J Phys Chem B
, vol.109
, pp. 17715-17733
-
-
Riccardi, D.1
Schaefer, P.2
Cui, Q.3
-
15
-
-
33846359282
-
An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations
-
Laino T., Mohamed F., Laio A., and Parrinello M. An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations. J Chem Theory Comput 2 (2006) 1370-1378
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 1370-1378
-
-
Laino, T.1
Mohamed, F.2
Laio, A.3
Parrinello, M.4
-
16
-
-
31544463548
-
Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps
-
König P.H., Ghosh N., Hoffmann M., Elstner M., Tajkhorshid E., Frauenheim T., and Cui Q. Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A 110 (2006) 548-563
-
(2006)
J Phys Chem A
, vol.110
, pp. 548-563
-
-
König, P.H.1
Ghosh, N.2
Hoffmann, M.3
Elstner, M.4
Tajkhorshid, E.5
Frauenheim, T.6
Cui, Q.7
-
17
-
-
15844379169
-
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
-
Banerjee A., Yang W., Karplus M., and Verdine G.L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434 (2005) 612-618
-
(2005)
Nature
, vol.434
, pp. 612-618
-
-
Banerjee, A.1
Yang, W.2
Karplus, M.3
Verdine, G.L.4
-
18
-
-
33747787695
-
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II
-
Hoffmann M., Wanko M., Strodel P., König P.H., Frauenheim T., Schulten K., Thiel W., Tajkhorshid E., and Elstner M. Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 128 (2006) 10808-10818
-
(2006)
J Am Chem Soc
, vol.128
, pp. 10808-10818
-
-
Hoffmann, M.1
Wanko, M.2
Strodel, P.3
König, P.H.4
Frauenheim, T.5
Schulten, K.6
Thiel, W.7
Tajkhorshid, E.8
Elstner, M.9
-
19
-
-
33748283200
-
The SCC-DFTB method and its application to biological systems
-
Elstner M. The SCC-DFTB method and its application to biological systems. Theor Chem Acc 116 (2006) 316-325
-
(2006)
Theor Chem Acc
, vol.116
, pp. 316-325
-
-
Elstner, M.1
-
20
-
-
33750478314
-
High-accuracy computation of reaction barriers in enzymes
-
Demonstration of the use of modern correlated ab initio methods in QM/MM calculations of enzymatic reaction barriers. LCCSD(T0) yields essentially chemical accuracy for the enzymes chorismate mutase and p-hydroxybenzoate hydroxylase.
-
Claeyssens F., Harvey J.N., Manby F.R., Mata R.A., Mulholland A.J., Ranaghan K.E., Schütz M., Thiel S., Thiel W., and Werner H.-J. High-accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed 45 (2006) 6856-6859. Demonstration of the use of modern correlated ab initio methods in QM/MM calculations of enzymatic reaction barriers. LCCSD(T0) yields essentially chemical accuracy for the enzymes chorismate mutase and p-hydroxybenzoate hydroxylase.
-
(2006)
Angew Chem Int Ed
, vol.45
, pp. 6856-6859
-
-
Claeyssens, F.1
Harvey, J.N.2
Manby, F.R.3
Mata, R.A.4
Mulholland, A.J.5
Ranaghan, K.E.6
Schütz, M.7
Thiel, S.8
Thiel, W.9
Werner, H.-J.10
-
21
-
-
2442573648
-
Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes
-
Xie L., Liu H., and Yang W. Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes. J Chem Phys 120 (2004) 8039-8052
-
(2004)
J Chem Phys
, vol.120
, pp. 8039-8052
-
-
Xie, L.1
Liu, H.2
Yang, W.3
-
22
-
-
3242703331
-
Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions
-
Liu H., Lu Z., Cisneros G.A., and Yang W. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. J Chem Phys 121 (2004) 697-706
-
(2004)
J Chem Phys
, vol.121
, pp. 697-706
-
-
Liu, H.1
Lu, Z.2
Cisneros, G.A.3
Yang, W.4
-
23
-
-
18644375413
-
Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order 'chain-of-replicas' methods
-
114502/1-7
-
Cisneros G.A., Liu H., Lu Z., and Yang W. Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order 'chain-of-replicas' methods. J Chem Phys (2005) 122 114502/1-7
-
(2005)
J Chem Phys
, pp. 122
-
-
Cisneros, G.A.1
Liu, H.2
Lu, Z.3
Yang, W.4
-
24
-
-
3142736515
-
Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations
-
Lu Z., and Yang W. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations. J Chem Phys 121 (2004) 89-100
-
(2004)
J Chem Phys
, vol.121
, pp. 89-100
-
-
Lu, Z.1
Yang, W.2
-
25
-
-
0000145441
-
Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
-
Zhang Y., Liu H., and Yang W. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J Chem Phys 112 (2000) 3483-3492
-
(2000)
J Chem Phys
, vol.112
, pp. 3483-3492
-
-
Zhang, Y.1
Liu, H.2
Yang, W.3
-
26
-
-
85051912728
-
Quantum mechanical free energy barrier for an enzymatic reaction
-
138302/1-4
-
Rod T.H., and Ryde U. Quantum mechanical free energy barrier for an enzymatic reaction. Phys Rev Lett 94 (2005) 138302/1-4
-
(2005)
Phys Rev Lett
, vol.94
-
-
Rod, T.H.1
Ryde, U.2
-
27
-
-
33646508010
-
Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase
-
Rod T.H., and Ryde U. Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase. J Chem Theory Comput 1 (2005) 1240-1251
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 1240-1251
-
-
Rod, T.H.1
Ryde, U.2
-
28
-
-
33745294923
-
QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction
-
Kästner J., Senn H.M., Thiel S., Otte N., and Thiel W. QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction. J Chem Theory Comput 2 (2006) 452-461
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 452-461
-
-
Kästner, J.1
Senn, H.M.2
Thiel, S.3
Otte, N.4
Thiel, W.5
-
29
-
-
0036667496
-
Quantum chemical geometry optimizations in proteins using crystallographic raw data
-
Ryde U., Olsen L., and Nilsson K. Quantum chemical geometry optimizations in proteins using crystallographic raw data. J Comput Chem 23 (2002) 1058-1070
-
(2002)
J Comput Chem
, vol.23
, pp. 1058-1070
-
-
Ryde, U.1
Olsen, L.2
Nilsson, K.3
-
30
-
-
33745727307
-
Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach
-
Rulíšek L., and Ryde U. Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. J Phys Chem B 110 (2006) 11511-11518
-
(2006)
J Phys Chem B
, vol.110
, pp. 11511-11518
-
-
Rulíšek, L.1
Ryde, U.2
-
32
-
-
32544451640
-
Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
-
Hsiao Y.-W., and Ryde U. Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods. Inorg Chim Acta 359 (2006) 1081-1092
-
(2006)
Inorg Chim Acta
, vol.359
, pp. 1081-1092
-
-
Hsiao, Y.-W.1
Ryde, U.2
-
33
-
-
33751504561
-
Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement
-
Yu N., Hayik S.A., Wang B., Liao N., Reynolds C.H., and Merz Jr. K.M. Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement. J Chem Theory Comput 2 (2006) 1057-1069
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 1057-1069
-
-
Yu, N.1
Hayik, S.A.2
Wang, B.3
Liao, N.4
Reynolds, C.H.5
Merz Jr., K.M.6
-
34
-
-
2342565009
-
Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction
-
Ranaghan K.E., Ridder L., Szefczyk B., Sokalski W.A., Hermann J.C., and Mulholland A.J. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction. Org Biomol Chem 2 (2004) 968-980
-
(2004)
Org Biomol Chem
, vol.2
, pp. 968-980
-
-
Ranaghan, K.E.1
Ridder, L.2
Szefczyk, B.3
Sokalski, W.A.4
Hermann, J.C.5
Mulholland, A.J.6
-
35
-
-
2942739060
-
Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase
-
Ranaghan K.E., and Mulholland A.J. Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase. Chem Commun (2004) 1238-1239
-
(2004)
Chem Commun
, pp. 1238-1239
-
-
Ranaghan, K.E.1
Mulholland, A.J.2
-
36
-
-
10344265555
-
Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field
-
Szefczyk B., Mulholland A.J., Ranaghan K.E., and Sokalski W.A. Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J Am Chem Soc 126 (2004) 16148-16159
-
(2004)
J Am Chem Soc
, vol.126
, pp. 16148-16159
-
-
Szefczyk, B.1
Mulholland, A.J.2
Ranaghan, K.E.3
Sokalski, W.A.4
-
37
-
-
27644492410
-
Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization
-
Multiple reaction profiles obtained at the B3LYP/CHARMM level support the concept of transition-state stabilization for the Claisen rearrangement in chorismate mutase.
-
Claeyssens F., Ranaghan K.E., Manby F.R., Harvey J.N., and Mulholland A.J. Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization. Chem Commun (2005) 5068-5070. Multiple reaction profiles obtained at the B3LYP/CHARMM level support the concept of transition-state stabilization for the Claisen rearrangement in chorismate mutase.
-
(2005)
Chem Commun
, pp. 5068-5070
-
-
Claeyssens, F.1
Ranaghan, K.E.2
Manby, F.R.3
Harvey, J.N.4
Mulholland, A.J.5
-
38
-
-
23244446189
-
A definitive mechanism for chorismate mutase
-
Zhang X., Zhang X., and Bruice T.C. A definitive mechanism for chorismate mutase. Biochemistry 44 (2005) 10443-10448
-
(2005)
Biochemistry
, vol.44
, pp. 10443-10448
-
-
Zhang, X.1
Zhang, X.2
Bruice, T.C.3
-
39
-
-
33645979392
-
The catalytic power of enzymes: conformational selection or transition state stabilization?
-
A kinetic view on enzyme catalysis. Catalytic proposals are connected with kinetic expressions representing the effect of conformational states and the rate constants in the enzyme and in solution. Chorismate mutase serves as illustrative example.
-
Giraldo J., Roche D., Rovira X., and Serra J. The catalytic power of enzymes: conformational selection or transition state stabilization?. FEBS Lett 580 (2006) 2170-2177. A kinetic view on enzyme catalysis. Catalytic proposals are connected with kinetic expressions representing the effect of conformational states and the rate constants in the enzyme and in solution. Chorismate mutase serves as illustrative example.
-
(2006)
FEBS Lett
, vol.580
, pp. 2170-2177
-
-
Giraldo, J.1
Roche, D.2
Rovira, X.3
Serra, J.4
-
40
-
-
21944432511
-
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes
-
Comprehensive review.
-
Shaik S., Kumar D., de Visser S.P., Altun A., and Thiel W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem Rev 105 (2005) 2279-2328. Comprehensive review.
-
(2005)
Chem Rev
, vol.105
, pp. 2279-2328
-
-
Shaik, S.1
Kumar, D.2
de Visser, S.P.3
Altun, A.4
Thiel, W.5
-
42
-
-
3142761726
-
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study
-
Guallar V., and Friesner R.A. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. J Am Chem Soc 126 (2004) 8501-8508
-
(2004)
J Am Chem Soc
, vol.126
, pp. 8501-8508
-
-
Guallar, V.1
Friesner, R.A.2
-
44
-
-
33747153306
-
Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor
-
Technically detailed report highlighting the possible pitfalls in QM/MM studies on enzyme reactivity.
-
Altun A., Shaik S., and Thiel W. Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor. J Comput Chem 27 (2006) 1324-1337. Technically detailed report highlighting the possible pitfalls in QM/MM studies on enzyme reactivity.
-
(2006)
J Comput Chem
, vol.27
, pp. 1324-1337
-
-
Altun, A.1
Shaik, S.2
Thiel, W.3
-
45
-
-
33749520822
-
QM/MM study of mechanisms for Compound I formation in the catalytic cycle of cytochrome P450cam
-
Zheng J., Wang D., Thiel W., and Shaik S. QM/MM study of mechanisms for Compound I formation in the catalytic cycle of cytochrome P450cam. J Am Chem Soc 128 (2006) 13204-13215
-
(2006)
J Am Chem Soc
, vol.128
, pp. 13204-13215
-
-
Zheng, J.1
Wang, D.2
Thiel, W.3
Shaik, S.4
-
46
-
-
25144520939
-
Electronic structure of Compound I in human isoforms of cytochrome P450 from QM/MM modeling
-
Bathelt C.M., Zurek J., Mulholland A.J., and Harvey J.N. Electronic structure of Compound I in human isoforms of cytochrome P450 from QM/MM modeling. J Am Chem Soc 127 (2005) 12900-12908
-
(2005)
J Am Chem Soc
, vol.127
, pp. 12900-12908
-
-
Bathelt, C.M.1
Zurek, J.2
Mulholland, A.J.3
Harvey, J.N.4
-
47
-
-
33644648714
-
In silico design of a mutant of cytochrome P450 containing selenocysteine
-
Cohen S., Kumar D., and Shaik S. In silico design of a mutant of cytochrome P450 containing selenocysteine. J Am Chem Soc 128 (2006) 2649-2653
-
(2006)
J Am Chem Soc
, vol.128
, pp. 2649-2653
-
-
Cohen, S.1
Kumar, D.2
Shaik, S.3
-
48
-
-
1842502916
-
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis isomerization of the chromophore in the protein
-
The excited-states dynamics of the photoactivated trans-to-cis isomerization of the PYP chromophore is investigated at the CASSCF/MM level using a surface-hopping algorithm. The reactivity after the photoevent is followed with classical MD and semi-empirical QM/MM. Results include quantum yields, fluorescence lifetimes and mechanistic insights, such as the preferential electrostatic stabilization of the chromophore's excited state in the active site.
-
Groenhof G., Bouxin-Cademartory M., Hess B., de Visser S.P., Berendsen H.J.C., Olivucci M., Mark A.E., and Robb M.A. Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis isomerization of the chromophore in the protein. J Am Chem Soc 126 (2004) 4228-4233. The excited-states dynamics of the photoactivated trans-to-cis isomerization of the PYP chromophore is investigated at the CASSCF/MM level using a surface-hopping algorithm. The reactivity after the photoevent is followed with classical MD and semi-empirical QM/MM. Results include quantum yields, fluorescence lifetimes and mechanistic insights, such as the preferential electrostatic stabilization of the chromophore's excited state in the active site.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 4228-4233
-
-
Groenhof, G.1
Bouxin-Cademartory, M.2
Hess, B.3
de Visser, S.P.4
Berendsen, H.J.C.5
Olivucci, M.6
Mark, A.E.7
Robb, M.A.8
-
49
-
-
23944508561
-
Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level
-
Sinicropi A., Andruniow T., Ferré N., Basosi R., and Olivucci M. Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc 127 (2005) 11534-11535
-
(2005)
J Am Chem Soc
, vol.127
, pp. 11534-11535
-
-
Sinicropi, A.1
Andruniow, T.2
Ferré, N.3
Basosi, R.4
Olivucci, M.5
-
51
-
-
33747189732
-
QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study
-
Sinnecker S., and Neese F. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study. J Comput Chem 27 (2006) 1463-1475
-
(2006)
J Comput Chem
, vol.27
, pp. 1463-1475
-
-
Sinnecker, S.1
Neese, F.2
-
52
-
-
17744364713
-
Toward identification of the Compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters
-
Schöneboom J.C., Neese F., and Thiel W. Toward identification of the Compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters. J Am Chem Soc 127 (2005) 5840-5853
-
(2005)
J Am Chem Soc
, vol.127
, pp. 5840-5853
-
-
Schöneboom, J.C.1
Neese, F.2
Thiel, W.3
|