-
1
-
-
4243606192
-
Unified approach for molecular-dynamics and density-functional theory
-
Car R., and Parrinello M. Unified approach for molecular-dynamics and density-functional theory. Phys Rev Lett 55 (1985) 2471-2474
-
(1985)
Phys Rev Lett
, vol.55
, pp. 2471-2474
-
-
Car, R.1
Parrinello, M.2
-
2
-
-
15344345714
-
QUICKSTEP: fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
-
VandeVondele J., Krack M., Mohamed F., Parrinello M., Chassaing T., and Hutter J. QUICKSTEP: fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Comput Phys Commun 167 (2005) 103-128
-
(2005)
Comput Phys Commun
, vol.167
, pp. 103-128
-
-
VandeVondele, J.1
Krack, M.2
Mohamed, F.3
Parrinello, M.4
Chassaing, T.5
Hutter, J.6
-
3
-
-
0017100947
-
Theoretical studies of enzymic reactions - dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme
-
Warshel A., and Levitt M. Theoretical studies of enzymic reactions - dielectric, electrostatic and steric stabilization of carbonium-ion in 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
-
4
-
-
0037156101
-
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
-
Laio A., VandeVondele J., and Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J Chem Phys 116 (2002) 6941-6947
-
(2002)
J Chem Phys
, vol.116
, pp. 6941-6947
-
-
Laio, A.1
VandeVondele, J.2
Rothlisberger, U.3
-
5
-
-
0000928098
-
A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields
-
Eichinger M., Tavan P., Hutter J., and Parrinello M. A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields. J Chem Phys 110 (1999) 10452-10467
-
(1999)
J Chem Phys
, vol.110
, pp. 10452-10467
-
-
Eichinger, M.1
Tavan, P.2
Hutter, J.3
Parrinello, M.4
-
6
-
-
0038136893
-
Why do divalent metal ions either promote or inhibit enzymatic reactions? - The case of BamHI restriction endonuclease from combined quantum-classical simulations
-
Mordasini T., Curioni A., and Andreoni W. Why do divalent metal ions either promote or inhibit enzymatic reactions? - The case of BamHI restriction endonuclease from combined quantum-classical simulations. J Biol Chem 278 (2003) 4381-4384
-
(2003)
J Biol Chem
, vol.278
, pp. 4381-4384
-
-
Mordasini, T.1
Curioni, A.2
Andreoni, W.3
-
7
-
-
34147124631
-
-
van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH,Krüger PKHC, Mark AE, Scott WRP, Tironi IG: Biomolecular simulation: The GROMOS96 manual and user guide. Zurich: vdf Hochschulverlag AG, 1996.
-
-
-
-
8
-
-
4444242987
-
On the calculation of reaction rate constants in the transition path ensemble
-
Dellago C., Bolhuis P.G., and Chandler D. On the calculation of reaction rate constants in the transition path ensemble. J Chem Phys 110 (1999) 6617-6625
-
(1999)
J Chem Phys
, vol.110
, pp. 6617-6625
-
-
Dellago, C.1
Bolhuis, P.G.2
Chandler, D.3
-
9
-
-
0001702831
-
Free energy from constrained molecular dynamics
-
Sprik M., and Ciccotti G. Free energy from constrained molecular dynamics. J Chem Phys 109 (1998) 7737-7744
-
(1998)
J Chem Phys
, vol.109
, pp. 7737-7744
-
-
Sprik, M.1
Ciccotti, G.2
-
11
-
-
0041810451
-
Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics
-
Iannuzzi M., Laio A., and Parrinello M. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys Rev Lett 90 (2003) 238302
-
(2003)
Phys Rev Lett
, vol.90
, pp. 238302
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
12
-
-
10044248161
-
A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations
-
Raugei S., Cascella M., and Carloni P. A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. J Am Chem Soc 126 (2004) 15730-15737
-
(2004)
J Am Chem Soc
, vol.126
, pp. 15730-15737
-
-
Raugei, S.1
Cascella, M.2
Carloni, P.3
-
13
-
-
15744387343
-
Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
-
The combination of multinanosecond MD and MM/CPMD simulations indicates that mechanical large-scale fluctuations exhibited by proteases are crucial for the modulation of the catalytic efficiency.
-
Cascella M., Micheletti C., Rothlisberger U., and Carloni P. Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. J Am Chem Soc 127 (2005) 3734-3742. The combination of multinanosecond MD and MM/CPMD simulations indicates that mechanical large-scale fluctuations exhibited by proteases are crucial for the modulation of the catalytic efficiency.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 3734-3742
-
-
Cascella, M.1
Micheletti, C.2
Rothlisberger, U.3
Carloni, P.4
-
14
-
-
0038675538
-
Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations
-
Sulpizi M., Laio A., VandeVondele J., Cattaneo A., Rothlisberger U., and Carloni P. Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations. Proteins 52 (2003) 212-224
-
(2003)
Proteins
, vol.52
, pp. 212-224
-
-
Sulpizi, M.1
Laio, A.2
VandeVondele, J.3
Cattaneo, A.4
Rothlisberger, U.5
Carloni, P.6
-
15
-
-
33644967069
-
Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase - insight from first principles molecular dynamics simulations
-
Biarnes X., Nieto J., Planas A., and Rovira C. Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase - insight from first principles molecular dynamics simulations. J Biol Chem 281 (2006) 1432-1441
-
(2006)
J Biol Chem
, vol.281
, pp. 1432-1441
-
-
Biarnes, X.1
Nieto, J.2
Planas, A.3
Rovira, C.4
-
16
-
-
33744901437
-
Deuterium isotope effects in A:T and A:U base pairs: a computational NMR study
-
Vidossich P., Piana S., Miani A., and Carloni P. Deuterium isotope effects in A:T and A:U base pairs: a computational NMR study. J Am Chem Soc 128 (2006) 7215-7221
-
(2006)
J Am Chem Soc
, vol.128
, pp. 7215-7221
-
-
Vidossich, P.1
Piana, S.2
Miani, A.3
Carloni, P.4
-
17
-
-
33750615201
-
Polarization effects and charge transfer in the KcsA potassium channel
-
+ selective filter suggest that the backbone carbonyl groups are largely polarized and that there is sizeable charge transfer from the backbone to the cations. These effects might be relevant for an accurate description of the electrostatic repulsion among the carbonyl groups and the cations, which has been proposed to play a central role in the selectivity mechanism of the channel [67].
-
+ selective filter suggest that the backbone carbonyl groups are largely polarized and that there is sizeable charge transfer from the backbone to the cations. These effects might be relevant for an accurate description of the electrostatic repulsion among the carbonyl groups and the cations, which has been proposed to play a central role in the selectivity mechanism of the channel [67].
-
(2006)
Biophys Chem
, vol.124
, pp. 292-301
-
-
Bucher, D.1
Raugei, S.2
Guidoni, L.3
Dal Peraro, M.4
Rothlisberger, U.5
Carloni, P.6
Klein, M.L.7
-
18
-
-
4744346992
-
Water-assisted reaction mechanism of monozinc β-lactamases
-
Dal Peraro M., Llarrull L.I., Rothlisberger U., Vila A.J., and Carloni P. Water-assisted reaction mechanism of monozinc β-lactamases. J Am Chem Soc 126 (2004) 12661-12668
-
(2004)
J Am Chem Soc
, vol.126
, pp. 12661-12668
-
-
Dal Peraro, M.1
Llarrull, L.I.2
Rothlisberger, U.3
Vila, A.J.4
Carloni, P.5
-
19
-
-
33947199145
-
Role of zinc content on the catalytic efficiency of B1 metallo β-lactamases
-
2+ ion in MβLs is discussed based on a direct and consistent comparison of monozinc and dizinc species.
-
2+ ion in MβLs is discussed based on a direct and consistent comparison of monozinc and dizinc species.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 2808-2816
-
-
Dal Peraro, M.1
Vila, A.J.2
Carloni, P.3
Klein, M.L.4
-
20
-
-
23844483422
-
Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle
-
De Vivo M., Ensing B., and Klein M.L. Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle. J Am Chem Soc 127 (2005) 11226-11227
-
(2005)
J Am Chem Soc
, vol.127
, pp. 11226-11227
-
-
De Vivo, M.1
Ensing, B.2
Klein, M.L.3
-
21
-
-
33846245591
-
Proton shuttles and phosphatase activity in soluble epoxide hydrolase
-
The crucial role of an ordered hydrogen-bond network of water molecules in phosphoryl transfer reactions emerges from this set of calculations. This suggests the general importance of explicitly including solvation effects at the catalytic site for the correct description of a reaction mechanism.
-
De Vivo M., Ensing B., Dal Peraro M., Gomez G.A., Christianson D.W., and Klein M.L. Proton shuttles and phosphatase activity in soluble epoxide hydrolase. J Am Chem Soc 129 (2007) 387-394. The crucial role of an ordered hydrogen-bond network of water molecules in phosphoryl transfer reactions emerges from this set of calculations. This suggests the general importance of explicitly including solvation effects at the catalytic site for the correct description of a reaction mechanism.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 387-394
-
-
De Vivo, M.1
Ensing, B.2
Dal Peraro, M.3
Gomez, G.A.4
Christianson, D.W.5
Klein, M.L.6
-
22
-
-
33845922101
-
2+ metal cations in the hydrolysis reaction
-
+ cations at the active site cooperate to activate this water via exchange between their solvation shells, sensibly improving the catalytic efficiency of formation of the inorganic phosphate.
-
+ cations at the active site cooperate to activate this water via exchange between their solvation shells, sensibly improving the catalytic efficiency of formation of the inorganic phosphate.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 16798-16807
-
-
Boero, M.1
Ikeda, T.2
Ito, E.3
Terakura, K.4
-
23
-
-
33645405625
-
A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
-
Rovira C., Alfonso-Prieto M., Biarnes X., Carpena X., Fita I., and Loewen P.C. A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures. Chem Phys 323 (2006) 129-137
-
(2006)
Chem Phys
, vol.323
, pp. 129-137
-
-
Rovira, C.1
Alfonso-Prieto, M.2
Biarnes, X.3
Carpena, X.4
Fita, I.5
Loewen, P.C.6
-
24
-
-
34147171814
-
The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM DFT calculations
-
10.1021/ja063660y
-
Alfonso-Prieto M., Borovik A., Carpena X., Mursnudov G., Melik-Adamyan W., Fita I., Rovira C., and Loewen P.C. The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM DFT calculations. J Am Chem Soc (2007) 10.1021/ja063660y
-
(2007)
J Am Chem Soc
-
-
Alfonso-Prieto, M.1
Borovik, A.2
Carpena, X.3
Mursnudov, G.4
Melik-Adamyan, W.5
Fita, I.6
Rovira, C.7
Loewen, P.C.8
-
25
-
-
33644893629
-
Structure and function of vanadium haloperoxidases
-
The rest state of the vanadium-dependent chloroperoxidases and the early stages of the catalytic cycle have been investigated by MM/CPMD metadynamics simulations. This is one of the first applications of metadynamics to a biological system within the MM/CPMD approach.
-
Raugei S., and Carloni P. Structure and function of vanadium haloperoxidases. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 110 (2006) 3747-3758. The rest state of the vanadium-dependent chloroperoxidases and the early stages of the catalytic cycle have been investigated by MM/CPMD metadynamics simulations. This is one of the first applications of metadynamics to a biological system within the MM/CPMD approach.
-
(2006)
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys
, vol.110
, pp. 3747-3758
-
-
Raugei, S.1
Carloni, P.2
-
26
-
-
33644970162
-
Double-metal-ion/single-metal-ion mechanisms of the cleavage reaction of ribozymes: first-principles molecular dynamics simulations of a fully hydrated model system
-
Boero M., Tateno M., Terakura K., and Oshiyama A. Double-metal-ion/single-metal-ion mechanisms of the cleavage reaction of ribozymes: first-principles molecular dynamics simulations of a fully hydrated model system. J Chem Theory Comput 1 (2005) 925-934
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 925-934
-
-
Boero, M.1
Tateno, M.2
Terakura, K.3
Oshiyama, A.4
-
27
-
-
33750624074
-
Metallo-β-lactamases: novel weaponry for antibiotic resistance in bacteria
-
Crowder M.W., Spencer J., and Vila A.J. Metallo-β-lactamases: novel weaponry for antibiotic resistance in bacteria. Acc Chem Res 39 (2006) 721-728
-
(2006)
Acc Chem Res
, vol.39
, pp. 721-728
-
-
Crowder, M.W.1
Spencer, J.2
Vila, A.J.3
-
28
-
-
2542422438
-
Structure, recognition, and processing of cisplatin-DNA adducts
-
Jamieson E.R., and Lippard S.J. Structure, recognition, and processing of cisplatin-DNA adducts. Chem Rev 99 (1999) 2467-2498
-
(1999)
Chem Rev
, vol.99
, pp. 2467-2498
-
-
Jamieson, E.R.1
Lippard, S.J.2
-
29
-
-
0037386291
-
New clues for platinum antitumor chemistry: kinetically controlled metal binding to DNA
-
Reedijk J. New clues for platinum antitumor chemistry: kinetically controlled metal binding to DNA. Proc Natl Acad Sci USA 100 (2003) 3611-3616
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3611-3616
-
-
Reedijk, J.1
-
30
-
-
1542305706
-
Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations
-
Extensive MM/CPMD simulations of cisplatin-DNA adducts succeed in shedding light on questions related to structural features extracted from X-ray and NMR data. In particular, the platinated DNA has been simulated in complex with the high mobility group protein domain A, pinpointing electronic and structural perturbations induced by complexation.
-
Spiegel K., Rothlisberger U., and Carloni P. Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations. J Phys Chem B 108 (2004) 2699-2707. Extensive MM/CPMD simulations of cisplatin-DNA adducts succeed in shedding light on questions related to structural features extracted from X-ray and NMR data. In particular, the platinated DNA has been simulated in complex with the high mobility group protein domain A, pinpointing electronic and structural perturbations induced by complexation.
-
(2004)
J Phys Chem B
, vol.108
, pp. 2699-2707
-
-
Spiegel, K.1
Rothlisberger, U.2
Carloni, P.3
-
31
-
-
0032580979
-
NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin
-
Gelasco A., and Lippard S.J. NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin. Biochemistry 37 (1998) 9230-9239
-
(1998)
Biochemistry
, vol.37
, pp. 9230-9239
-
-
Gelasco, A.1
Lippard, S.J.2
-
32
-
-
33644977537
-
Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations
-
MM/CPMD calculations have identified the electronic origin of the isomerization process involving a new platinum-derived drug, confirming the suggestion made on the basis of experimental data. The process enlarges the range of possible drug-DNA linkages and could cooperate in lowering drug resistance.
-
Magistrato A., Ruggerone P., Spiegel K., Carloni P., and Reedijk J. Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 110 (2006) 3604-3613. MM/CPMD calculations have identified the electronic origin of the isomerization process involving a new platinum-derived drug, confirming the suggestion made on the basis of experimental data. The process enlarges the range of possible drug-DNA linkages and could cooperate in lowering drug resistance.
-
(2006)
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys
, vol.110
, pp. 3604-3613
-
-
Magistrato, A.1
Ruggerone, P.2
Spiegel, K.3
Carloni, P.4
Reedijk, J.5
-
33
-
-
0035822755
-
[Ru(eta(6)-p-cymene)Cl-2(pta)] (pta=1,3,5-triaza-7-phosphatricyclo[3. 3. 1. 1]decane): a water soluble compound that exhibits pH dependent DNA binding providing selectivity for diseased cells
-
Allardyce C.S., Dyson P.J., Ellis D.J., and Heath S.L. [Ru(eta(6)-p-cymene)Cl-2(pta)] (pta=1,3,5-triaza-7-phosphatricyclo[3. 3. 1. 1]decane): a water soluble compound that exhibits pH dependent DNA binding providing selectivity for diseased cells. Chem Commun (2001) 1396-1397
-
(2001)
Chem Commun
, pp. 1396-1397
-
-
Allardyce, C.S.1
Dyson, P.J.2
Ellis, D.J.3
Heath, S.L.4
-
34
-
-
17444362297
-
Rational design of organo-ruthenium anticancer compounds
-
Gossens C., Tavemelli I., and Rothlisberger U. Rational design of organo-ruthenium anticancer compounds. Chimia (Aarau) 59 (2005) 81-84
-
(2005)
Chimia (Aarau)
, vol.59
, pp. 81-84
-
-
Gossens, C.1
Tavemelli, I.2
Rothlisberger, U.3
-
35
-
-
0141706614
-
DNA interactions of monofunctional organometallic ruthenium(II) antitumor complexes in cell-free media
-
Novakova O., Chen H.M., Vrana O., Rodger A., Sadler P.J., and Brabec V. DNA interactions of monofunctional organometallic ruthenium(II) antitumor complexes in cell-free media. Biochemistry 42 (2003) 11544-11554
-
(2003)
Biochemistry
, vol.42
, pp. 11544-11554
-
-
Novakova, O.1
Chen, H.M.2
Vrana, O.3
Rodger, A.4
Sadler, P.J.5
Brabec, V.6
-
36
-
-
33644557736
-
Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study
-
Vidossich P., and Carloni P. Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 110 (2006) 1437-1442
-
(2006)
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys
, vol.110
, pp. 1437-1442
-
-
Vidossich, P.1
Carloni, P.2
-
38
-
-
21344450916
-
Study of ligand-protein interactions by means of density functional theory and first-principles molecular dynamics
-
Rovira C. Study of ligand-protein interactions by means of density functional theory and first-principles molecular dynamics. Methods Mol Biol 305 (2005) 517-554
-
(2005)
Methods Mol Biol
, vol.305
, pp. 517-554
-
-
Rovira, C.1
-
39
-
-
0347625834
-
2 vs CO-heme: a time-dependent density functional study
-
2 vs CO-heme: a time-dependent density functional study. J Am Chem Soc 125 (2003) 15710-15711
-
(2003)
J Am Chem Soc
, vol.125
, pp. 15710-15711
-
-
De Angelis, F.1
Car, R.2
Spiro, T.G.3
-
40
-
-
33748334301
-
Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach
-
Transition metal complexes, usually problematic within DFT, benefit from a generalized-gradient approximation augmented by a Hubbard term (U), which is determined by a new self-consistent procedure based on linear response theory. This computationally efficient scheme provides remarkable improvements for spin energetics, state symmetries and reaction barriers, and represents a promising step towards an accurate theoretical description of transition-metal-based biochemistry.
-
Kulik H.J., Cococcioni M., Scherlis D.A., and Marzari N. Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach. Phys Rev Lett 97 (2006) 103001. Transition metal complexes, usually problematic within DFT, benefit from a generalized-gradient approximation augmented by a Hubbard term (U), which is determined by a new self-consistent procedure based on linear response theory. This computationally efficient scheme provides remarkable improvements for spin energetics, state symmetries and reaction barriers, and represents a promising step towards an accurate theoretical description of transition-metal-based biochemistry.
-
(2006)
Phys Rev Lett
, vol.97
, pp. 103001
-
-
Kulik, H.J.1
Cococcioni, M.2
Scherlis, D.A.3
Marzari, N.4
-
41
-
-
33748444599
-
Structure and dynamics of dioxygen bound to cobalt and iron heme
-
Degtyarenko I., Nieminen R.M., and Rovira C. Structure and dynamics of dioxygen bound to cobalt and iron heme. Biophys J 91 (2006) 2024-2034
-
(2006)
Biophys J
, vol.91
, pp. 2024-2034
-
-
Degtyarenko, I.1
Nieminen, R.M.2
Rovira, C.3
-
42
-
-
11244349605
-
The mechanism of long-distance radical cation transport in duplex DNA: ion-gated hopping of polaron-like distortions
-
Schuster G.B., and Landman U. The mechanism of long-distance radical cation transport in duplex DNA: ion-gated hopping of polaron-like distortions. Top Curr Chem 236 (2004) 139-161
-
(2004)
Top Curr Chem
, vol.236
, pp. 139-161
-
-
Schuster, G.B.1
Landman, U.2
-
45
-
-
29144447300
-
Strain-dependence of the electronic properties in periodic quadruple helical G4-wires
-
Di Felice R., Calzolari A., Garbesi A., Alexandre S.S., and Soler J.M. Strain-dependence of the electronic properties in periodic quadruple helical G4-wires. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 109 (2005) 22301-22307
-
(2005)
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys
, vol.109
, pp. 22301-22307
-
-
Di Felice, R.1
Calzolari, A.2
Garbesi, A.3
Alexandre, S.S.4
Soler, J.M.5
-
47
-
-
5444274109
-
Influence of DNA structure on the reactivity of the guanine radical cation
-
Gervasio F.L., Laio A., Iannuzzi M., and Parrinello M. Influence of DNA structure on the reactivity of the guanine radical cation. Chemistry 10 (2004) 4846-4852
-
(2004)
Chemistry
, vol.10
, pp. 4846-4852
-
-
Gervasio, F.L.1
Laio, A.2
Iannuzzi, M.3
Parrinello, M.4
-
48
-
-
0037206801
-
Irradiated guanine: a Car-Parrinello molecular dynamics study of dehydrogenation in the presence of an OH radical
-
Mundy C.J., Colvin M.E., and Quong A.A. Irradiated guanine: a Car-Parrinello molecular dynamics study of dehydrogenation in the presence of an OH radical. J Phys Chem A 106 (2002) 10063-10071
-
(2002)
J Phys Chem A
, vol.106
, pp. 10063-10071
-
-
Mundy, C.J.1
Colvin, M.E.2
Quong, A.A.3
-
49
-
-
0010884753
-
Theory of oxidation-reduction reactions involving electron transfer.1
-
Marcus R.A. Theory of oxidation-reduction reactions involving electron transfer.1. J Chem Phys 24 (1956) 966-978
-
(1956)
J Chem Phys
, vol.24
, pp. 966-978
-
-
Marcus, R.A.1
-
50
-
-
36849118773
-
On theory of electron-transfer reactions. 6. Unified treatment for homogeneous and electrode reactions
-
Marcus R.A. On theory of electron-transfer reactions. 6. Unified treatment for homogeneous and electrode reactions. J Chem Phys 43 (1965) 679
-
(1965)
J Chem Phys
, vol.43
, pp. 679
-
-
Marcus, R.A.1
-
51
-
-
0007836334
-
Dynamics of reactions in polar-solvents - semi-classical trajectory studies of electron-transfer and proton-transfer reactions
-
Warshel A. Dynamics of reactions in polar-solvents - semi-classical trajectory studies of electron-transfer and proton-transfer reactions. J Phys Chem 86 (1982) 2218-2224
-
(1982)
J Phys Chem
, vol.86
, pp. 2218-2224
-
-
Warshel, A.1
-
52
-
-
0037182390
-
Ab initio molecular dynamics for molecules with variable numbers of electrons
-
Tavernelli I., Vuilleumier R., and Sprik M. Ab initio molecular dynamics for molecules with variable numbers of electrons. Phys Rev Lett 88 (2002) 213002
-
(2002)
Phys Rev Lett
, vol.88
, pp. 213002
-
-
Tavernelli, I.1
Vuilleumier, R.2
Sprik, M.3
-
54
-
-
23344447224
-
Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes
-
Tateyama Y., Blumberger J., Sprik M., and Tavernelli I. Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes. J Chem Phys 122 (2005) 234505
-
(2005)
J Chem Phys
, vol.122
, pp. 234505
-
-
Tateyama, Y.1
Blumberger, J.2
Sprik, M.3
Tavernelli, I.4
-
55
-
-
1642276658
-
Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction
-
Blumberger J., Bernasconi L., Tavernelli I., Vuilleumier R., and Sprik M. Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction. J Am Chem Soc 126 (2004) 3928-3938
-
(2004)
J Am Chem Soc
, vol.126
, pp. 3928-3938
-
-
Blumberger, J.1
Bernasconi, L.2
Tavernelli, I.3
Vuilleumier, R.4
Sprik, M.5
-
56
-
-
33845935792
-
Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa
-
MM/CPMD simulations coupled to a grand-canonical scheme have been performed to study the Cu(II)/Cu(I) half-reaction in azurin from P. aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and thermal fluctuations of the protein structure are both essential for a correct quantitative description of the redox properties of the system. The redox potential is fine-tuned by long-range electrostatic interactions, whereas the reorganization energy is mainly due to solvent rearrangement at the protein surface.
-
Cascella M., Magistrato A., Tavernelli I., Carloni P., and Rothlisberger U. Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa. Proc Natl Acad Sci USA 103 (2006) 19641-19646. MM/CPMD simulations coupled to a grand-canonical scheme have been performed to study the Cu(II)/Cu(I) half-reaction in azurin from P. aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and thermal fluctuations of the protein structure are both essential for a correct quantitative description of the redox properties of the system. The redox potential is fine-tuned by long-range electrostatic interactions, whereas the reorganization energy is mainly due to solvent rearrangement at the protein surface.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 19641-19646
-
-
Cascella, M.1
Magistrato, A.2
Tavernelli, I.3
Carloni, P.4
Rothlisberger, U.5
-
57
-
-
33750285531
-
Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein
-
The authors have computed the reorganization free energy for both oxidation of a single Ru-porphyrin cofactor and electron self-exchange between two Ru-porphyrin cofactors binding to a solvated four-helix-bundle protein. Through accurate sampling of the classical electrostatic energy gap, they find that the fluctuations are well described by Gaussian statistics. Decomposing the outer-sphere reorganization free energy, they found that the solvent (aqueous ionic solution) is the primary outer-sphere medium for oxidation, whereas the protein contributes only for a smaller fraction.
-
Blumberger J., and Klein M.L. Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein. J Am Chem Soc 128 (2006) 13854-13867. The authors have computed the reorganization free energy for both oxidation of a single Ru-porphyrin cofactor and electron self-exchange between two Ru-porphyrin cofactors binding to a solvated four-helix-bundle protein. Through accurate sampling of the classical electrostatic energy gap, they find that the fluctuations are well described by Gaussian statistics. Decomposing the outer-sphere reorganization free energy, they found that the solvent (aqueous ionic solution) is the primary outer-sphere medium for oxidation, whereas the protein contributes only for a smaller fraction.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 13854-13867
-
-
Blumberger, J.1
Klein, M.L.2
-
58
-
-
34247868775
-
-
Sulpizi M, Raugei S, VandeVondele J, Sprik M, Carloni P: Calculation of redox properties: understanding short and long range effects in rubredoxin. J Phys Chem B 2007, in press. The experimental redox potential difference between mesophilic and thermophilic rubredoxin is explained in terms of short-range contributions from a few residues close to the metal center. It is also proposed that the protein controls the reorganization free energy in a balance between shielding of the high dielectric solvent medium and preserving some water accessibility to the metal center for fast electron transfer to the surface. These results underline the importance of a molecular description of the solvent and of correct inclusion of the polarization effects.
-
-
-
-
61
-
-
17144388610
-
A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods
-
VandeVondele J., and Sprik M. A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods. Phys Chem Chem Phys 7 (2005) 1363-1367
-
(2005)
Phys Chem Chem Phys
, vol.7
, pp. 1363-1367
-
-
VandeVondele, J.1
Sprik, M.2
-
62
-
-
34147116967
-
Automated parametrization of biomolecular force fields from QM/MM simulations through force-matching
-
A recipe to parameterize biomolecular systems 'on the fly' via first principles MM/CPMD simulations is presented in this paper. The generation of DFT-based parameters for simulating metal-containing proteins for which standard force fields poorly perform can largely improve the accuracy of current MD simulations.
-
Maurer P., Laio A., Hugossonz H., Colombo M.C., and Rothlisberger U. Automated parametrization of biomolecular force fields from QM/MM simulations through force-matching. J Chem Theory Comput 3 (2007) 628-639. A recipe to parameterize biomolecular systems 'on the fly' via first principles MM/CPMD simulations is presented in this paper. The generation of DFT-based parameters for simulating metal-containing proteins for which standard force fields poorly perform can largely improve the accuracy of current MD simulations.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 628-639
-
-
Maurer, P.1
Laio, A.2
Hugossonz, H.3
Colombo, M.C.4
Rothlisberger, U.5
-
63
-
-
34147096159
-
-
Spiegel K, Magistrato A, Maurer P, Ruggerone P, Rothlisberger U, Carloni P, Reedijk J, Klein ML: Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. J Comput Chem 2007, in press.
-
-
-
-
64
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching
-
Izvekov S., Parrinello M., Burnham C.J., and Voth G.A. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J Chem Phys 120 (2004) 10896-10913
-
(2004)
J Chem Phys
, vol.120
, pp. 10896-10913
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
65
-
-
19644400832
-
Optimization of effective atom centered potentials for London dispersion forces in density functional theory
-
Using an efficient algorithm, dispersion forces are included in DFT-based calculations at essentially no additional computational cost. The van der Waals forces are modeled by an atom-electron interaction, instead of approximating them via an atom-atom term. Thus, a remarkable improvement in the description of molecular properties within the DFT framework is achieved.
-
von Lilienfeld O.A., Tavernelli I., Rothlisberger U., and Sebastiani D. Optimization of effective atom centered potentials for London dispersion forces in density functional theory. Phys Rev Lett 93 (2004) 153004. Using an efficient algorithm, dispersion forces are included in DFT-based calculations at essentially no additional computational cost. The van der Waals forces are modeled by an atom-electron interaction, instead of approximating them via an atom-atom term. Thus, a remarkable improvement in the description of molecular properties within the DFT framework is achieved.
-
(2004)
Phys Rev Lett
, vol.93
, pp. 153004
-
-
von Lilienfeld, O.A.1
Tavernelli, I.2
Rothlisberger, U.3
Sebastiani, D.4
-
67
-
-
7244251461
-
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
-
Noskov S.Y., Berneche S., and Roux B. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-833
-
(2004)
Nature
, vol.431
, pp. 830-833
-
-
Noskov, S.Y.1
Berneche, S.2
Roux, B.3
-
68
-
-
0034683460
-
New antitumor-active azole-bridged dinuclear platinum(II) complexes: synthesis, characterization, crystal structures, and cytotoxic studies
-
Komeda S., Lutz M., Spek A.L., Chikuma M., and Reedijk J. New antitumor-active azole-bridged dinuclear platinum(II) complexes: synthesis, characterization, crystal structures, and cytotoxic studies. Inorg Chem 39 (2000) 4230-4236
-
(2000)
Inorg Chem
, vol.39
, pp. 4230-4236
-
-
Komeda, S.1
Lutz, M.2
Spek, A.L.3
Chikuma, M.4
Reedijk, J.5
-
69
-
-
0035913970
-
Charge migration in DNA: ion-gated transport
-
Barnett R.N., Cleveland C.L., Joy A., Landman U., and Schuster G.B. Charge migration in DNA: ion-gated transport. Science 294 (2001) 567-571
-
(2001)
Science
, vol.294
, pp. 567-571
-
-
Barnett, R.N.1
Cleveland, C.L.2
Joy, A.3
Landman, U.4
Schuster, G.B.5
-
70
-
-
33748578676
-
Double proton coupled charge transfer in DNA
-
Based on CPMD and MM/CPMD calculations, the authors point to a key role for rare DNA tautomers in charge transfer processes in DNA.
-
Gervasio F.L., Boero M., and Parrinello M. Double proton coupled charge transfer in DNA. Angew Chem Int Ed Engl 45 (2006) 5606-5609. Based on CPMD and MM/CPMD calculations, the authors point to a key role for rare DNA tautomers in charge transfer processes in DNA.
-
(2006)
Angew Chem Int Ed Engl
, vol.45
, pp. 5606-5609
-
-
Gervasio, F.L.1
Boero, M.2
Parrinello, M.3
-
71
-
-
0035913290
-
Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling
-
Giese B., Amaudrut J., Kohler A.K., Spormann M., and Wessely S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature 412 (2001) 318-320
-
(2001)
Nature
, vol.412
, pp. 318-320
-
-
Giese, B.1
Amaudrut, J.2
Kohler, A.K.3
Spormann, M.4
Wessely, S.5
-
72
-
-
33846891132
-
Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics
-
The authors introduce an improved dynamics in which the CP equation of motion is replaced by an integration scheme (via an accurate predictor-corrector algorithm) to maintain the electrons as close as possible to the instantaneous ground state. The resulting dynamics is very accurate in terms of sampling distribution and deviation from the Born-Oppenheimer (BO) surface, and accelerated by at least one order of magnitude with respect to current CPMD and BOMD.
-
Kühne T.D., Krack M., Mohamed F.R., and Parrinello M. Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics. Phys Rev Lett 98 (2007) 066401. The authors introduce an improved dynamics in which the CP equation of motion is replaced by an integration scheme (via an accurate predictor-corrector algorithm) to maintain the electrons as close as possible to the instantaneous ground state. The resulting dynamics is very accurate in terms of sampling distribution and deviation from the Born-Oppenheimer (BO) surface, and accelerated by at least one order of magnitude with respect to current CPMD and BOMD.
-
(2007)
Phys Rev Lett
, vol.98
, pp. 066401
-
-
Kühne, T.D.1
Krack, M.2
Mohamed, F.R.3
Parrinello, M.4
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