-
1
-
-
0002617092
-
Portrait of an allosteric protein
-
Freeman, New York, NY
-
Stryer, L. (1997) Portrait of an allosteric protein, in: Biochemistry, Freeman, New York, NY, pp. 147–180.
-
(1997)
Biochemistry
, pp. 147-180
-
-
Stryer, L.1
-
2
-
-
33845282119
-
Stereochemistry of cooperative mechanisms in hemoglobin
-
Perutz, M. F., Fermi, G., Luisi, B., Shaanan, B., and Liddington, R. C. (1987) Stereochemistry of cooperative mechanisms in hemoglobin. Acc. Chem. Res. 20, 309–321.
-
(1987)
Acc. Chem. Res
, vol.20
, pp. 309-321
-
-
Perutz, M. F.1
Fermi, G.2
Luisi, B.3
Shaanan, B.4
Liddington, R. C.5
-
3
-
-
0033596859
-
Examination of the nickel site structure and reaction mechanism in Streptomyces seoulensis superoxide dismutase
-
Choudhury, S. B., Lee, J.-W., Davidson, G., Yim, Y.-I., Bose, K., Sharma, M. L., Kang, S.-O., Cabelli, D. E., and Maroney, M. J. (1999) Examination of the nickel site structure and reaction mechanism in Streptomyces seoulensis superoxide dismutase. Biochemistry 38, 3744–3752.
-
(1999)
Biochemistry
, vol.38
, pp. 3744-3752
-
-
Choudhury, S. B.1
Lee, J.-W.2
Davidson, G.3
Yim, Y.-I.4
Bose, K.5
Sharma, M. L.6
Kang, S.-O.7
Cabelli, D. E.8
Maroney, M. J.9
-
6
-
-
4243606192
-
Unified approach for molecular dynamics and density-functional theory
-
Car, R. and Parrinello, M. (1985) Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55, 2471–2474.
-
(1985)
Phys. Rev. Lett
, vol.55
, pp. 2471-2474
-
-
Car, R.1
Parrinello, M.2
-
7
-
-
0344791553
-
Approximate Density Functional Theory as a practical tool in molecular energetics and dynamics
-
Ziegler, T. (1991) Approximate Density Functional Theory as a practical tool in molecular energetics and dynamics. Chem. Rev. 91, 651–667.
-
(1991)
Chem. Rev
, vol.91
, pp. 651-667
-
-
Ziegler, T.1
-
8
-
-
0242314692
-
The Kohn-Sham approach
-
Wiley-VCH, Weinheim, Germany
-
Koch, W. and Holthausen, M. C. (2000) The Kohn-Sham approach, in: A Chemist’s Guide to Density Functional Theory. Wiley-VCH, Weinheim, Germany, pp. 41–64.
-
(2000)
A Chemist’s Guide to Density Functional Theory
, pp. 41-64
-
-
Koch, W.1
Holthausen, M. C.2
-
9
-
-
0000074308
-
Molecular dynamics in low-spin excited states
-
Frank, I., Hutter, J., Marx, D., and Parrinello, M. (1998) Molecular dynamics in low-spin excited states. J. Chem. Phys. 108, 4060–4069.
-
(1998)
J. Chem. Phys
, vol.108
, pp. 4060-4069
-
-
Frank, I.1
Hutter, J.2
Marx, D.3
Parrinello, M.4
-
10
-
-
0032577087
-
Spin-restricted density functional approach to the open-shell problem
-
Filatov, M. and Shaik, S. (1998) Spin-restricted density functional approach to the open-shell problem. Chem. Phys. Lett. 288, 689–697.
-
(1998)
Chem. Phys. Lett
, vol.288
, pp. 689-697
-
-
Filatov, M.1
Shaik, S.2
-
11
-
-
0003849463
-
-
(Seminario, J. M., ed) Elsevier, Amsterdam, The Netherlands
-
Casida, M. E. (1996) in: Recent Developments and Applications of Modern Denisty Functional Theory. ( Seminario, J. M., ed.) Elsevier, Amsterdam, The Netherlands.
-
(1996)
Recent Developments and Applications of Modern Denisty Functional Theory
-
-
Casida, M. E.1
-
12
-
-
0000790755
-
van der Waals energies in Density Functional Theory
-
Kohn, W., Meir, Y., and Makarov, D. (1998) van der Waals energies in Density Functional Theory. Phys. Rev. Lett. 80, 4153–4156.
-
(1998)
Phys. Rev. Lett
, vol.80
, pp. 4153-4156
-
-
Kohn, W.1
Meir, Y.2
Makarov, D.3
-
13
-
-
0035932162
-
Hydrogen bonding and stacking interactions of nucleic acid base pairs: a density-func-tional-theory based treatment
-
Eltsner, M., Hobza, P., Frauenheim, T., Suhai, S., and Kaxiras, E. (2001) Hydrogen bonding and stacking interactions of nucleic acid base pairs: a density-func-tional-theory based treatment. J. Chem. Phys. 114, 5149–5155.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 5149-5155
-
-
Eltsner, M.1
Hobza, P.2
Frauenheim, T.3
Suhai, S.4
Kaxiras, E.5
-
14
-
-
19044387407
-
Electronic structure of wet DNA
-
105
-
Gervasio, F. L., Carloni, P., and Parrinello, M. (2002) Electronic structure of wet DNA. Phys. Rev. Lett. 89, 108,102–108,105.
-
(2002)
Phys. Rev. Lett
, vol.89
, Issue.108
, pp. 102-108
-
-
Gervasio, F. L.1
Carloni, P.2
Parrinello, M.3
-
15
-
-
4243810035
-
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
-
Aqvist, J. and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem. Rev. 93, 2523–2544.
-
(1993)
Chem. Rev
, vol.93
, pp. 2523-2544
-
-
Aqvist, J.1
Warshel, A.2
-
16
-
-
0037156101
-
A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
-
Laio, A., VandeVondele, J., and Rothlisberger, U. (2002) A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations, J. Chem. Phys. 116, 6941–6947.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 6941-6947
-
-
Laio, A.1
VandeVondele, J.2
Rothlisberger, U.3
-
17
-
-
0000730460
-
Selfconsistent order-N density-functional calculations for very large systems
-
Ordejon, P., Artacho, E., and Soler, J. M. (1996) Selfconsistent order-N density-functional calculations for very large systems. Phys. Rev. B. 53, R10441.
-
(1996)
Phys. Rev. B
, vol.53
, pp. R10441
-
-
Ordejon, P.1
Artacho, E.2
Soler, J. M.3
-
18
-
-
0041810451
-
Efficient exploration of reactive potential energy surfaces using Car–Parrinello molecular dynamics
-
Iannuzzi, M., Laio, A., and Parrinello, M. (2003) Efficient exploration of reactive potential energy surfaces using Car–Parrinello molecular dynamics, Phys. Rev. Lett. 90, 238–302.
-
(2003)
Phys. Rev. Lett
, vol.90
, pp. 238-302
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
19
-
-
0001181339
-
Density Functional Theory of biologically relevant metal centers
-
Siegbahn, P. E. and Blomberg, M. R. A. (1999) Density Functional Theory of biologically relevant metal centers, Annu. Rev. Phys. Chem. 50, 221–249.
-
(1999)
Annu. Rev. Phys. Chem
, vol.50
, pp. 221-249
-
-
Siegbahn, P. E.1
Blomberg, M. R. A.2
-
20
-
-
0032054613
-
Quantum mechanical calculations on biological systems
-
Friesner, R. A. and Beachy, M. D. (1998) Quantum mechanical calculations on biological systems. Curr. Op. Str. Biol. 8, 257–262.
-
(1998)
Curr. Op. Str. Biol
, vol.8
, pp. 257-262
-
-
Friesner, R. A.1
Beachy, M. D.2
-
21
-
-
0036286854
-
The role and perspective of ab initio molecular dynamics in the study of biological systems
-
Carloni, P., Röthlisberger, U., and Parrinello, M. (2002) The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc. Chem. Res. 35, 45–464.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 45-464
-
-
Carloni, P.1
Röthlisberger, U.2
Parrinello, M.3
-
22
-
-
0038305457
-
Quantum chemical studies of radical-containing enzymes
-
Himo, F. and Siegbahn, P. E. M. (2003) Quantum chemical studies of radical-containing enzymes. Chem. Rev. 103, 242–2456.
-
(2003)
Chem. Rev
, vol.103
, pp. 242-2456
-
-
Himo, F.1
Siegbahn, P. E. M.2
-
23
-
-
0037366128
-
Principles governing Mg, Ca, and Zn binding and selectivity in proteins
-
Dudev, T. and Lim, C. (2003) Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem. Rev. 103, 773–787.
-
(2003)
Chem. Rev
, vol.103
, pp. 773-787
-
-
Dudev, T.1
Lim, C.2
-
25
-
-
0035124398
-
The flexibility of carboxylate ligands in methane monooxygenase and ribonucleotide reductase: a density functional study
-
Torrent, M., Musaev, D. G., and Morokuma, K. (2001) The flexibility of carboxylate ligands in methane monooxygenase and ribonucleotide reductase: a density functional study. J. Phys. Chem. 105, 322–327.
-
(2001)
J. Phys. Chem
, vol.105
, pp. 322-327
-
-
Torrent, M.1
Musaev, D. G.2
Morokuma, K.3
-
26
-
-
0036306459
-
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
-
Piana, S., Carloni, P., and Parrinello, M. (2002) Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol. 319, 567–583.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 567-583
-
-
Piana, S.1
Carloni, P.2
Parrinello, M.3
-
27
-
-
0037071785
-
Potassium permeation through the KcsA channel: a density functional study
-
Guidoni, L. and Carloni, P. (2002) Potassium permeation through the KcsA channel: a density functional study. Biochim. Biophys. Acta 1563, 1–6.
-
(2002)
Biochim. Biophys. Acta
, vol.1563
, pp. 1-6
-
-
Guidoni, L.1
Carloni, P.2
-
28
-
-
0029775587
-
Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A
-
Sagnella D. E., Laasonen K., and Klein M. L. (1996) Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. Biophys. J. 71, 1172–1178.
-
(1996)
Biophys. J
, vol.71
, pp. 1172-1178
-
-
Sagnella, D. E.1
Laasonen, K.2
Klein, M. L.3
-
29
-
-
2342666659
-
Modeling protonated water networks in bacteriorhodopsin
-
Rousseau, R., Kleinschmidt, V., Schmitt, U. W., and Marx, D. (2004) Modeling protonated water networks in bacteriorhodopsin. Phys. Chem. Chem. Phys. 6, 1848–1859.
-
(2004)
Phys. Chem. Chem. Phys
, vol.6
, pp. 1848-1859
-
-
Rousseau, R.1
Kleinschmidt, V.2
Schmitt, U. W.3
Marx, D.4
-
30
-
-
0035023569
-
How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data
-
Stec, B. and Phillips, G. N. (2001) How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data. Acta Cryst. D57, 751–754.
-
(2001)
Acta Cryst
, vol.D57
, pp. 751-754
-
-
Stec, B.1
Phillips, G. N.2
-
31
-
-
0001588361
-
Functional analogs of heme protein active sites
-
Collman, J. P. (1997). Functional analogs of heme protein active sites. Inorg.Chem. 36, 5145–5155.
-
(1997)
Inorg.Chem
, vol.36
, pp. 5145-5155
-
-
Collman, J. P.1
-
32
-
-
33748590497
-
Carbonyl tilting and bending potential energy surface of carbon monoxyhemes
-
Ghosh, A. and Bocian, D. F. (1996) Carbonyl tilting and bending potential energy surface of carbon monoxyhemes. J. Phys. Chem. 100, 6363–6367.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 6363-6367
-
-
Ghosh, A.1
Bocian, D. F.2
-
33
-
-
0031276121
-
Equilibrium geometries and electronic structure of iron-porphyrin complexes: a density functional study
-
Rovira, C., Kunc, K., Hutter, J., Ballone, P., and Parrinello, M. (1997) Equilibrium geometries and electronic structure of iron-porphyrin complexes: a density functional study. J. Phys. Chem. A. 101, 8914–8925.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 8914-8925
-
-
Rovira, C.1
Kunc, K.2
Hutter, J.3
Ballone, P.4
Parrinello, M.5
-
34
-
-
0001397162
-
Discordant results on FeCO deform-ability in heme proteins reconciled by density functional theory
-
Spiro, T. G. and Kozlowski, P. M. (1998) Discordant results on FeCO deform-ability in heme proteins reconciled by density functional theory. J. Am. Chem. Soc. 120, 4524–4525.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 4524-4525
-
-
Spiro, T. G.1
Kozlowski, P. M.2
-
35
-
-
0038296982
-
The structure and dynamics of the Fe–CO bond in myoglobin
-
Rovira, C. (2003) The structure and dynamics of the Fe–CO bond in myoglobin. J. Phys. Cond. Mat. 15, 1809–1822.
-
(2003)
J. Phys. Cond. Mat
, vol.15
, pp. 1809-1822
-
-
Rovira, C.1
-
36
-
-
0029647452
-
Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe–C–O
-
Lim, M., Jackson, T. A., and Anfinrud, P. A. (1995) Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe–C–O. Science 269, 962–966.
-
(1995)
Science
, vol.269
, pp. 962-966
-
-
Lim, M.1
Jackson, T. A.2
Anfinrud, P. A.3
-
38
-
-
0000901899
-
17 O NMR chemical shift and nuclear quadrupole coupling tensors in oxyheme model complexes
-
17 O NMR chemical shift and nuclear quadrupole coupling tensors in oxyheme model complexes. J. Phys. Chem. B. 104, 5200–5208.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 5200-5208
-
-
Kaupp, M.1
Rovira, C.2
Parrinello, M.3
-
39
-
-
0037168603
-
Spin-dependent mechanism for duatomic ligand binding to heme
-
759
-
Franzen, S. (2002) Spin-dependent mechanism for duatomic ligand binding to heme. Proc. Nat. Acad. Sci. 99, 16,754–16,759.
-
(2002)
Proc. Nat. Acad. Sci
, vol.99
, Issue.16
, pp. 754-16
-
-
Franzen, S.1
-
40
-
-
0346365000
-
Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons
-
788
-
De Visser, S. P., Shaik, S., Sharma, P. K., Kumar, D., and Thiel, W. (2003) Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons. J. Am. Chem. Soc. 125, 15,779–15,788.
-
(2003)
J. Am. Chem. Soc
, vol.125
, Issue.15
, pp. 779-15
-
-
De Visser, S. P.1
Shaik, S.2
Sharma, P. K.3
Kumar, D.4
Thiel, W.5
-
41
-
-
0041654852
-
Modulation of NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase
-
Martí, M. A., Scherlis, D. A., Doctorovich, F. A., Ordejón, P., and Estrin, D. A. (2003) Modulation of NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase. J. Biol. Inorg. Chem. 8, 595–600.
-
(2003)
J. Biol. Inorg. Chem
, vol.8
, pp. 595-600
-
-
Martí, M. A.1
Scherlis, D. A.2
Doctorovich, F. A.3
Ordejón, P.4
Estrin, D. A.5
-
42
-
-
1542743893
-
Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 Å resolution
-
Loewen, P. C., Carpena, X., Rovira, C., Ivancich, A., Perez-Luque, R., Haas, R., Odenbreit, S., Nichols, P., and Fita., I. (2004) Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 Å resolution. Biochemistry 43, 3089–3103.
-
(2004)
Biochemistry
, vol.43
, pp. 3089-3103
-
-
Loewen, P. C.1
Carpena, X.2
Rovira, C.3
Ivancich, A.4
Perez-Luque, R.5
Haas, R.6
Odenbreit, S.7
Nichols, P.8
Fita., I.9
-
43
-
-
0027482810
-
Ligand binding to heme proteins. II. Transitions in the heme pocket of myoglobin
-
Mourant, J. R., Braunstein, D., Chu, K., Frauenfelder, H., Nienhaus, G. U., Ormos, P., and Young, R. D. (1993) Ligand binding to heme proteins. II. Transitions in the heme pocket of myoglobin. Biophys. J. 65, 1496–1507.
-
(1993)
Biophys. J
, vol.65
, pp. 1496-1507
-
-
Mourant, J. R.1
Braunstein, D.2
Chu, K.3
Frauenfelder, H.4
Nienhaus, G. U.5
Ormos, P.6
Young, R. D.7
-
44
-
-
0000519270
-
Combined quantum mechanical and molecular mechanical potentials
-
(Schleyer, P. R., Allinger, N. L., Clark, T., Gasteiget, J., Kollman, P. A., Schaefer III, H. F., Schreiner, P. R., eds) John Wiley & Sons, Chichester, UK
-
Amara, P. and Field, M. (1998) Combined quantum mechanical and molecular mechanical potentials, in: Encyclopedia of computational chemistry (Schleyer, P. v. R., Allinger, N. L., Clark, T., Gasteiget, J., Kollman, P. A., Schaefer III, H. F., Schreiner, P. R., eds.) John Wiley & Sons, Chichester, UK.
-
(1998)
Encyclopedia of computational chemistry
-
-
Amara, P.1
Field, M.2
-
45
-
-
0001763714
-
Frontier bonds in QM/ MM methods: A comparison of different approaches
-
Reuter, N., Dejaegere, A., Maigret, B., and Karplus, M. (2000) Frontier bonds in QM/ MM methods: A comparison of different approaches. J. Phys. Chem. A 104, 1720–1735.
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 1720-1735
-
-
Reuter, N.1
Dejaegere, A.2
Maigret, B.3
Karplus, M.4
-
46
-
-
0037156101
-
A hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
-
Laio, A., VandeVondele, J., and Röthlisberger, U. (2002) A hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J. Chem. Phys. 116, 6941–6947.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 6941-6947
-
-
Laio, A.1
VandeVondele, J.2
Röthlisberger, U.3
-
47
-
-
0038003758
-
Characterization of the dizinc analogue of the synthetic diiron DF1 using an initio hybrid quantum/classical molecular dynamics simulations
-
Magistrato, A., DeGrado, W., Laio, A., Röthlisberger, U., VandeVondele, J., and Klein, M. L. (2003) Characterization of the dizinc analogue of the synthetic diiron DF1 using an initio hybrid quantum/classical molecular dynamics simulations. J. Phys. Chem. B. 107, 4182–4188.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 4182-4188
-
-
Magistrato, A.1
DeGrado, W.2
Laio, A.3
Röthlisberger, U.4
VandeVondele, J.5
Klein, M. L.6
-
48
-
-
0034951055
-
Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin. A QM/MM density functional study
-
Rovira. C., Schulze, B., Eichinger, M., Evanseck, J. D., and Parrinello, M. (2001) Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin. A QM/MM density functional study. Biophys. J. 81, 435–445.
-
(2001)
Biophys. J
, vol.81
, pp. 435-445
-
-
Rovira., C.1
Schulze, B.2
Eichinger, M.3
Evanseck, J. D.4
Parrinello, M.5
-
49
-
-
0037055032
-
The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations
-
Schöneboom, J. C., Lin, H., Reuter, N., Thiel, W., Cohen, S., Ogliaro, F., and Shaik, S. (2002) The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. J. Am. Chem. Soc. 124, 8142–8151.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 8142-8151
-
-
Schöneboom, J. C.1
Lin, H.2
Reuter, N.3
Thiel, W.4
Cohen, S.5
Ogliaro, F.6
Shaik, S.7
-
50
-
-
85194600863
-
-
CPMD program, Copyright IBM Corp. 1990–2003, Copyright MPI für Festkörperforschung, Stuttgart 1997-2001
-
CPMD program, Copyright IBM Corp. 1990–2003, Copyright MPI für Festkörperforschung, Stuttgart 1997-2001. URL: http://www.cpmd.org.
-
-
-
-
51
-
-
10644250257
-
Inhomogeneous electron gas
-
Hohenberg, P. and Kohn, W. (1964) Inhomogeneous electron gas. Phys. Rev. B 136, 864–871.
-
(1964)
Phys. Rev. B
, vol.136
, pp. 864-871
-
-
Hohenberg, P.1
Kohn, W.2
-
52
-
-
0042113153
-
Self-consistent equations including exchange and correlation effects
-
Kohn, W. and Sham, L. J. (1965) Self-consistent equations including exchange and correlation effects. Phys. Rev. A. 140, 1133–1138.
-
(1965)
Phys. Rev. A
, vol.140
, pp. 1133-1138
-
-
Kohn, W.1
Sham, L. J.2
-
53
-
-
0242314692
-
The quest for approximate exchange-correlation functionals
-
Wiley-VCH, Weinheim, Germany
-
Koch, W. and Holthausen, M. C. (2000) The quest for approximate exchange-correlation functionals, in: A Chemist’s Guide to Density Functional Theory, Wiley-VCH, Weinheim, Germany, pp. 65–91.
-
(2000)
A Chemist’s Guide to Density Functional Theory
, pp. 65-91
-
-
Koch, W.1
Holthausen, M. C.2
-
54
-
-
0038472283
-
Ligand dynamics in a protein internal cavity
-
Kriegl, J. M., Nienhaus, K., Deng, P., Fuchs, J., and Nienhaus, G. U. (2003) Ligand dynamics in a protein internal cavity. Proc. Natl. Acad. Sci. 100, 7069– 7074.
-
(2003)
Proc. Natl. Acad. Sci
, vol.100
, pp. 7069-7074
-
-
Kriegl, J. M.1
Nienhaus, K.2
Deng, P.3
Fuchs, J.4
Nienhaus, G. U.5
-
55
-
-
0039892284
-
Density functional calculations of molecular bond energies
-
Becke, A. D. (1986) Density functional calculations of molecular bond energies. J. Chem. Phys. 84, 4524–4529.
-
(1986)
J. Chem. Phys
, vol.84
, pp. 4524-4529
-
-
Becke, A. D.1
-
56
-
-
5944261746
-
Density-functional approximation for the correlation energy of the inhomogeneous electron gas
-
Perdew, J. P. (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B. 33, 8822–8824.
-
(1986)
Phys. Rev. B
, vol.33
, pp. 8822-8824
-
-
Perdew, J. P.1
-
57
-
-
0345491105
-
Development of the Colle–Salvetti correla-tion-energy formula into a functional of electron density
-
Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle–Salvetti correla-tion-energy formula into a functional of electron density. Phys. Rev. B. 37, 785–789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R. G.3
-
58
-
-
4243943295
-
Generalized gradient approximation made simple
-
Erratum: (1997) Phys. Rev. Lett. 78, 1396
-
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996) Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868, Erratum: (1997) Phys. Rev. Lett. 78, 1396.
-
(1996)
Phys. Rev. Lett
, vol.77
, pp. 3865-3868
-
-
Perdew, J. P.1
Burke, K.2
Ernzerhof, M.3
-
59
-
-
34250817103
-
A new mixing of Hartree–Fock and local density-functional theories
-
Becke, A. D. (1993) A new mixing of Hartree–Fock and local density-functional theories. J. Chem. Phys. 98, 5648–5652.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 5648-5652
-
-
Becke, A. D.1
-
60
-
-
11944256577
-
Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients
-
Payne, M. C., Teter, M. P., Allan, D. C., Arias, T. A., and Joannopoulos, J. D. (1992) Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients. Rev. Mod. Phys. 64, 1045–1097.
-
(1992)
Rev. Mod. Phys
, vol.64
, pp. 1045-1097
-
-
Payne, M. C.1
Teter, M. P.2
Allan, D. C.3
Arias, T. A.4
Joannopoulos, J. D.5
-
61
-
-
4143095330
-
Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions
-
Kendall, R. A., Dunning, T. H., Jr., and Harrison, R. J. (1992) Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 96, 6796–6806.
-
(1992)
J. Chem. Phys
, vol.96
, pp. 6796-6806
-
-
Kendall, R. A.1
Dunning, T. H.2
Harrison, R. J.3
-
62
-
-
33646638059
-
Pseudopotential methods in condensed matter applications
-
Pickett, W. E. (1989) Pseudopotential methods in condensed matter applications Comput. Phys. Rep. 9, 115–197.
-
(1989)
Comput. Phys. Rep
, vol.9
, pp. 115-197
-
-
Pickett, W. E.1
-
63
-
-
0000323669
-
Ab initio molecular dynamics: theory and implementation
-
(Grotendorst, J., ed), John von Neumann Institute for Computing, Julich, Germany
-
Marx, D. and Hutter, J. (2000) Ab initio molecular dynamics: theory and implementation, in: Modern methods and algorithms of Quantum Chemistry (Grotendorst, J., ed.), John von Neumann Institute for Computing, Julich, Germany, pp. 301–409.
-
(2000)
Modern methods and algorithms of Quantum Chemistry
, pp. 301-409
-
-
Marx, D.1
Hutter, J.2
-
64
-
-
22944467757
-
Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet, L. (1967) Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98–103.
-
(1967)
Phys. Rev
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
65
-
-
0009822387
-
Comment on ”error cancelation in the molecular dynamics method for total energy calculations
-
Car, R., Parrinello, M., and Payne, M. (1991) Comment on ”error cancelation in the molecular dynamics method for total energy calculations.” J. Phys. Cond. Matt. 3, 9539–9543.
-
(1991)
J. Phys. Cond. Matt
, vol.3
, pp. 9539-9543
-
-
Car, R.1
Parrinello, M.2
Payne, M.3
-
66
-
-
84947362301
-
Molecular dynamics without effective potentials via the Car–Parrinello approach
-
Remler, D. K. and Madden, P. A. (1990) Molecular dynamics without effective potentials via the Car–Parrinello approach. Mol. Phys. 70, 921–966.
-
(1990)
Mol. Phys
, vol.70
, pp. 921-966
-
-
Remler, D. K.1
Madden, P. A.2
-
67
-
-
0036025449
-
Ab initio molecular dynamics with density functional theory
-
Tse, J. S. (2002) Ab initio molecular dynamics with density functional theory. Annu. Rev. Phys. Chem. 53, 24–290.
-
(2002)
Annu. Rev. Phys. Chem
, vol.53
, pp. 24-290
-
-
Tse, J. S.1
-
68
-
-
0037139291
-
Structure and spin-state energetics of an iron–porphyrin model: An assessment of theoretical methods
-
Scherlis, D. A. and Estrin, D. A. (2002) Structure and spin-state energetics of an iron–porphyrin model: An assessment of theoretical methods. Int. J. Quant. Chem. 87, 158–166.
-
(2002)
Int. J. Quant. Chem
, vol.87
, pp. 158-166
-
-
Scherlis, D. A.1
Estrin, D. A.2
-
69
-
-
0141959727
-
Theoretical prediction of the Co–C bond strength in cobalamins
-
Jensen, K. and Ryde, U. (2003) Theoretical prediction of the Co–C bond strength in cobalamins. J. Phys. Chem. A. 107, 7539–7545.
-
(2003)
J. Phys. Chem. A
, vol.107
, pp. 7539-7545
-
-
Jensen, K.1
Ryde, U.2
-
70
-
-
33645426115
-
Efficient pseudopotentials for plane-wave calculations
-
Troullier, M. and Martins, J. L. (1991) Efficient pseudopotentials for plane-wave calculations, Phys. ReV. B 43, 1993–2006.
-
(1991)
Phys. ReV. B
, vol.43
, pp. 1993-2006
-
-
Troullier, M.1
Martins, J. L.2
-
71
-
-
0000549623
-
Non-linear ionic pseudopotentials in spin-density-functional calculations
-
Louie, S. G., Froyen, S., and Cohen, M. L. (1982) Non-linear ionic pseudopotentials in spin-density-functional calculations, Phys. Rev. B. 26, 1738–1742.
-
(1982)
Phys. Rev. B
, vol.26
, pp. 1738-1742
-
-
Louie, S. G.1
Froyen, S.2
Cohen, M. L.3
-
72
-
-
0038853525
-
Crystal structures of myoglobin-ligand complexes at near-atomic resolution
-
Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R. M., and Schlichting, I. (1999) Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Biophys. J. 77, 2153–2174.
-
(1999)
Biophys. J
, vol.77
, pp. 2153-2174
-
-
Vojtechovsky, J.1
Chu, K.2
Berendzen, J.3
Sweet, R. M.4
Schlichting, I.5
-
73
-
-
0019942576
-
The iron–oxygen bond in human oxyhaemoglobin
-
Shaanan, B. (1982) The iron–oxygen bond in human oxyhaemoglobin. Nature 296, 683–684.
-
(1982)
Nature
, vol.296
, pp. 683-684
-
-
Shaanan, B.1
-
74
-
-
0001622166
-
Structure of a dyoxygen adduct of (1-methylimidazole)-meso-tetrakis(α,α,α,α−ο-pivalamidophenyl) porphinatoiron(II). An iron dioxygen model for the heme component of oxymyoglobin
-
Jameson, G. B., Rodley, G. A., Robinson, W. T., Gagne, R. R., Reed, C. A., and Collman, J. P. (1978). Structure of a dyoxygen adduct of (1-methylimidazole)-meso-tetrakis(α,α,α,α−ο-pivalamidophenyl) porphinatoiron(II). An iron dioxygen model for the heme component of oxymyoglobin. Inorg. Chem. 17, 850–857.
-
(1978)
Inorg. Chem
, vol.17
, pp. 850-857
-
-
Jameson, G. B.1
Rodley, G. A.2
Robinson, W. T.3
Gagne, R. R.4
Reed, C. A.5
Collman, J. P.6
-
75
-
-
0000564803
-
Models for the active site of oxygen-binding hemoproteins. Dioxygen binding properties and the structures of (2-methylimidazole)-meso-tetra(α,α,α,α−ο−pivalamidophenyl)poprhyrinatoiron(II)-ethanol and its dioxygen adduct
-
Jameson, G. B., Molinaro, F., Ibers, J. A., Collman, J. P., Brauman, J. I., Rose, E., and Suslick, K. S. (1980) Models for the active site of oxygen-binding hemoproteins. Dioxygen binding properties and the structures of (2-methylimidazole)-meso-tetra(α,α,α,α−ο−pivalamidophenyl)poprhyrinatoiron(II)-ethanol and its dioxygen adduct. J. Am. Chem. Soc. 102, 3224–3237.
-
(1980)
J. Am. Chem. Soc
, vol.102
, pp. 3224-3237
-
-
Jameson, G. B.1
Molinaro, F.2
Ibers, J. A.3
Collman, J. P.4
Brauman, J. I.5
Rose, E.6
Suslick, K. S.7
-
76
-
-
0020749147
-
O2 and CO binding to iron(II) porphyrins: a comparison of the “picket fence” and “pocket” porphyrins
-
Collman, J. P., Brauman, J. I., Iverson, B. L., Sessler, J. L., Morris, R. M., and Gibson, Q. H. (1983) O2 and CO binding to iron(II) porphyrins: a comparison of the “picket fence” and “pocket” porphyrins. J. Am. Chem. Soc. 105, 3052–3064.
-
(1983)
J. Am. Chem. Soc
, vol.105
, pp. 3052-3064
-
-
Collman, J. P.1
Brauman, J. I.2
Iverson, B. L.3
Sessler, J. L.4
Morris, R. M.5
Gibson, Q. H.6
-
77
-
-
0018544682
-
Oxygen binding to myoglobin and their cobalt analogs
-
Wang, M. R., Hoffman, B. M., Shire, S. J., and Gurd, F. R. N. (1979) Oxygen binding to myoglobin and their cobalt analogs. J. Am. Chem. Soc. 101, 7394–7397.
-
(1979)
J. Am. Chem. Soc
, vol.101
, pp. 7394-7397
-
-
Wang, M. R.1
Hoffman, B. M.2
Shire, S. J.3
Gurd, F. R. N.4
-
78
-
-
0002424327
-
Nature of the iron-oxygen bond in oxyhemoglobin
-
Weiss, J. J. (1964) Nature of the iron-oxygen bond in oxyhemoglobin. Nature (London) 202, 83–84.
-
(1964)
Nature (London)
, vol.202
, pp. 83-84
-
-
Weiss, J. J.1
-
79
-
-
37049049612
-
Nature of the iron-oxygen bond in oxyhemoglobin
-
Pauling, L. (1964) Nature of the iron-oxygen bond in oxyhemoglobin. Nature (London) 203, 182–183.
-
(1964)
Nature (London)
, vol.203
, pp. 182-183
-
-
Pauling, L.1
-
80
-
-
0017902203
-
2 – coupling at the active center
-
2 – coupling at the active center. Z. Naturforsch 33, 488–494.
-
(1978)
Z. Naturforsch
, vol.33
, pp. 488-494
-
-
Bade, D.1
Parak, F.2
-
81
-
-
3042907629
-
Synthetic heme-dioxygen complexes
-
Momenteau, M. and Reed, C. A. (1994) Synthetic heme-dioxygen complexes Chem. Rev. 94, 659–698.
-
(1994)
Chem. Rev
, vol.94
, pp. 659-698
-
-
Momenteau, M.1
Reed, C. A.2
-
82
-
-
0012904850
-
A theoretical investigation of the magnetic and ground-state properties of model oxyhemoglobin complexes
-
Herman, Z. S. and Loew, G. H. (1980) A theoretical investigation of the magnetic and ground-state properties of model oxyhemoglobin complexes. J. Am. Chem. Soc. 102, 1815–1821.
-
(1980)
J. Am. Chem. Soc
, vol.102
, pp. 1815-1821
-
-
Herman, Z. S.1
Loew, G. H.2
-
83
-
-
0001415426
-
CASSCF calculation on dioxygen heme complex with extended basis set
-
Yamamoto, S. and Kashiwagi, H. (1993) CASSCF calculation on dioxygen heme complex with extended basis set. Chem. Phys. Lett. 205, 306–312.
-
(1993)
Chem. Phys. Lett
, vol.205
, pp. 306-312
-
-
Yamamoto, S.1
Kashiwagi, H.2
-
84
-
-
0001512013
-
Oxygen binding to iron-porphyrin: a Density functional study using both LSD and LSD+GC schemes
-
Rovira, C. and Parrinello, M. (1998) Oxygen binding to iron-porphyrin: a Density functional study using both LSD and LSD+GC schemes. Int. J. Quant. Chem. 70, 387–394.
-
(1998)
Int. J. Quant. Chem
, vol.70
, pp. 387-394
-
-
Rovira, C.1
Parrinello, M.2
-
85
-
-
0021027685
-
Structure of human oxyhaemoglobin at 2.1 Å resolution
-
Shaanan, B. (1983). Structure of human oxyhaemoglobin at 2.1 Å resolution. J. Mol. Biol. 171, 31–59.
-
(1983)
J. Mol. Biol
, vol.171
, pp. 31-59
-
-
Shaanan, B.1
-
86
-
-
0001740216
-
Mössbauer spectroscopy of hemoglobin model compounds: evidence for conformational excitation
-
Spartalian, K., Lang, G., Collman, J. P., Gagne, R. R., and Reed, C. A. (1975) Mössbauer spectroscopy of hemoglobin model compounds: evidence for conformational excitation. J. Chem. Phys. 63, 5375–5382.
-
(1975)
J. Chem. Phys
, vol.63
, pp. 5375-5382
-
-
Spartalian, K.1
Lang, G.2
Collman, J. P.3
Gagne, R. R.4
Reed, C. A.5
-
87
-
-
0039358601
-
Hydrogen-bond stabilization of oxygen in hemoprotein models
-
Mispelter, J., Momenteau, M., Lavalette, D., and Lhoste, J.-M. (1983) Hydrogen-bond stabilization of oxygen in hemoprotein models. J. Am.Chem. Soc. 105, 5165–5166.
-
(1983)
J. Am.Chem. Soc
, vol.105
, pp. 5165-5166
-
-
Mispelter, J.1
Momenteau, M.2
Lavalette, D.3
Lhoste, J.-M.4
-
88
-
-
0000833977
-
17 O] picket-fence porphyrin, myoglobin, and hemoglobin
-
17 O] picket-fence porphyrin, myoglobin, and hemoglobin. J. Am. Chem. Soc. 113, 8680–8685.
-
(1991)
J. Am. Chem. Soc
, vol.113
, pp. 8680-8685
-
-
Oldfield, E.1
Lee, H. C.2
Coretsopoulos, C.3
Adebodum, F.4
Park, K. D.5
Yang, S.6
Chung, J.7
Phillips, B.8
-
89
-
-
0031245896
-
EPR studies of the dynamics of rotation of dioxygen in model cobalt(II) hemes and cobalt-containing hybrid hemoglobins
-
Bowen, J. H., Shokhirev, N. V., Raitsimring, A. M., Buttlaire, D. H., and Walker, F. A. (1997) EPR studies of the dynamics of rotation of dioxygen in model cobalt(II) hemes and cobalt-containing hybrid hemoglobins. J. Am. Chem. Soc. 101, 8683–8691.
-
(1997)
J. Am. Chem. Soc
, vol.101
, pp. 8683-8691
-
-
Bowen, J. H.1
Shokhirev, N. V.2
Raitsimring, A. M.3
Buttlaire, D. H.4
Walker, F. A.5
-
90
-
-
35448998145
-
Enzymology and structure of cata-lases
-
Nicholls, P., Fita, I., and Loewen, P. C. (2001) Enzymology and structure of cata-lases, Adv. Inorg. Chem. 51, 51–106.
-
(2001)
Adv. Inorg. Chem
, vol.51
, pp. 51-106
-
-
Nicholls, P.1
Fita, I.2
Loewen, P. C.3
-
91
-
-
1542297780
-
The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemi-cal properties
-
Xu, X. and Goddard III, W. A. (2004) The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemi-cal properties. Proc. Nat. Acad. Sci. USA 101, 2673–2677.
-
(2004)
Proc. Nat. Acad. Sci. USA
, vol.101
, pp. 2673-2677
-
-
Xu, X.1
Goddard, W. A.2
-
92
-
-
0001161603
-
Efficacious form for model pseudopotentials
-
Kleinman, L. and Bylander, D. M. (1982) Efficacious form for model pseudopotentials Phys. Rev. Lett. 48, 1425–1428.
-
(1982)
Phys. Rev. Lett
, vol.48
, pp. 1425-1428
-
-
Kleinman, L.1
Bylander, D. M.2
-
93
-
-
84986524957
-
Convergence acceleration of iterative sequences. The case of scf iteration
-
Pulay, P. (1980) Convergence acceleration of iterative sequences. The case of scf iteration. Chem. Phys. Lett. 73, 393–398.
-
(1980)
Chem. Phys. Lett
, vol.73
, pp. 393-398
-
-
Pulay, P.1
-
94
-
-
20644461001
-
On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a poste-riori BSSE correction schemes
-
Salvador, P., Paizs, B., Duran, M., and Suhai, S. (2001) On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a poste-riori BSSE correction schemes. J. Comp. Chem. 22, 765–786.
-
(2001)
J. Comp. Chem
, vol.22
, pp. 765-786
-
-
Salvador, P.1
Paizs, B.2
Duran, M.3
Suhai, S.4
-
95
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nosé. S. (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255–268.
-
(1984)
Mol. Phys
, vol.52
, pp. 255-268
-
-
|