Introduction to theory/modeling methods in photosynthesis

Photosynthesis Research

Volumn 102, Issue 2, 2009, Pages 437-441

  Buda, Francesco ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

DFT; Free energy calculations; Molecular dynamics; Multi scale simulations; QMMM

Indexed keywords

BIOLOGICAL MODEL; MOLECULAR DYNAMICS; PHOTOSYNTHESIS; PHYSIOLOGY; QUANTUM THEORY; REVIEW;

MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; PHOTOSYNTHESIS; QUANTUM THEORY;

EID: 76149124193     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11120-009-9476-5     Document Type: Review

References (31)

1. Alia A, Wawrzyniak PK, Janssen G, Buda F, Matysik J, de Groot HJM (2009) Differential charge polarization of axial histidines in bacterial reaction centres balances the asymmetry of the special pair. J Am Chem Soc 131: 9626-9627. doi: 10. 1021/ja9028507.
2. Atkins PW, Friedman RS (2005) Molecular quantum mechanics. Oxford University Press, New York.
3. Car R, Parrinello M (1985) Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55: 2471-2474.
4. Cramer CJ (2002) Essentials of computational chemistry-Theories and models. Wiley, Chichester.
5. Damjanovic A, Kosztin I, Kleinekathofer U, Schulten K (2002) Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study. Phys Rev E 65: 031919-1-031919-24.
6. Dreizler RM, Gross EKV (1990) Density functional theory. Springer, Berlin.
7. Filippi C, Zaccheddu M, Buda F (2009) The absorption spectrum of the green fluorescent protein chromophore: a difficult case for ab initio methods? J Chem Theory Comput. doi: 10. 1021/ct900227j.
8. Frenkel D, Smit B (1996) Understanding molecular simulation-From algorithms to applications. Academic Press, San Diego.
9. Ganapathy S, Oostergetel G, Wawrzyniak PK, Reus M, Gomez A, Chew M, Buda F, Boekema E, Holzwarth A, Bryant D, de Groot HJM (2009a) Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes. PNAS 106: 8525-8530.
10. Ganapathy S, Sengupta S, Wawrzyniak PK, Huber V, Buda F, Baumeister U, Würthner F, de Groot HJM (2009b) Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material. PNAS 106: 11472-11477.
11. Gruning M, Gritsenko OV, Baerends EJ (2004) Improved description of chemical barriers with generalized gradient approximations (GGAs) and meta-GGAs. J Phys Chem A 108: 4459-4469.
12. Herrmann C, Podewitz M, Reiher M (2009) Restrained optimization of broken-symmetry determinants. Int J Quantum Chem 109: 2430-2446.
13. Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev B 136: 864-871.
14. Klein ML, Shinoda W (2008) Large-scale molecular dynamics simulations of self-assembling systems. Science 321: 798-800.
15. Kosztin I, Schulten K (2008) Molecular dynamics methods for bioelectronic systems in photosynthesis. In: Aartsma TJ, Matysik J (eds) Biophysical techniques in photosynthesis, vol 2, Series advances in photosynthesis and respiration, vol 26. Springer, Dordrecht, pp 445-464.
16. Laio A, Parrinello M (2002) Escaping free-energy minima. PNAS 99: 12562-12566.
17. Lin H, Truhlar DG (2007) QM/MM: what have we learned, where are we, and where do we go from here? Theory Chem Acc 117: 185-199.
18. 2: design principles of photosystem II and hydrogenases. Energy Environ Sci 1: 15-31.
19. Neugebauer J (2008) Photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory. J Phys Chem B 112: 2207-2217.
20. Parson WW, Warshel A (2008) Calculations of electrostatic energies in proteins using microscopic, semimicroscopic and macroscopic models and free-energy perturbation approaches. In: Aartsma TJ, Matysik J (eds) Biophysical techniques in photosynthesis, vol 2, Series advances in photosynthesis and respiration, vol 26. Springer, Dordrecht, pp 401-420.
21. Parson WW, Chu ZT, Warshel A (1998) Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers. Biophys J 74: 182-191.
22. Renger T, Holzwarth AR (2008) Theory of excitation energy transfer and optical spectra of photosynthetic systems. In: Aartsma TJ, Matysik J (eds) Biophysical techniques in photosynthesis, vol 2, Series advances in photosynthesis and respiration, vol 26. Springer, Dordrecht, pp 421-443.
23. Rossmeisl J, Logadottir A, Nørskov JK (2005) Electrolysis of water on (oxidized) metal surfaces. Chem Phys 319: 178-184.
24. Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52: 997-1000.
25. Sherwood P (2000) Hybrid quantum mechanics/molecular mechanics approaches. In: Grotendorst J (ed) Modern methods and algorithms of quantum chemistry, vol 1. NIC Series, Jülich, pp 257-277.
26. Siegbahn PEM (2008) A structure-consistent mechanism for dioxygen formation in photosystem II. Chem Eur J 14: 8290-8302.
27. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS (2008) QM/MM study of the catalytic cycle of water splitting in photosystem II. J Am Chem Soc 130: 3428-3442.
28. Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley, New York.
29. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilisation of the carbonium ion in the reaction of lysozyme. J Mol Biol 103: 227-249.
30. Warshel A, Parson WW (2001) Dynamics of biochemical and biophysical reactions: insight from computer simulations. Q Rev Biophys 34: 563-679.
31. Wawrzyniak PK, Alia A, Schaap RG, Heemskerk MM, de Groot HJM, Buda F (2008) Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2. Phys Chem Chem Phys 10: 6971-6978.