Description of excited states in photochemistry with theoretical methods

References

[1] Schmidt T, et al. QM/MM investigations of organic chemistry oriented questions. Berlin/Heidelberg: Springer, 2012:1–77.10.1007/128_2011_309Suche in Google Scholar PubMed

[2] González L, Escudero D, Serrano-Andrés L. Progress and challenges in the calculation of electronic excited states. Chemphyschem Eur J Chem Phy Phy Chem. 2012;13:28–51.10.1002/cphc.201100200Suche in Google Scholar PubMed

[3] Bernardi F, Olivucci M, Robb MA. Potential energy surface crossings in organic photochemistry. Chem Soc Rev. 1996;25:321–8.10.1039/cs9962500321Suche in Google Scholar

[4] Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem. 2003;66:27–85.10.1016/S0065-3233(03)66002-XSuche in Google Scholar PubMed

[5] Senn HM, Thiel W. QM/MM methods for biological systems. Reiher M, editors. Vol. 268, Berlin/Heidelberg: Springer, 2007:173–290.10.1007/128_2006_084Suche in Google Scholar

[6] Born M, Oppenheimer R. Zur Quantentheorie der Molekeln. Ann Phys. 1927;389:457–84.10.1007/978-3-642-61659-4_16Suche in Google Scholar

[7] Teller E. The crossing of potential surfaces. J Phys Chem. 1937;41:109–16.10.1021/j150379a010Suche in Google Scholar

[8] Domcke W, Woywod C. Direct construction of diabetic states in the CASSCF approach. Application to the conical intersection of the 1A2 and 1B1 excited states of ozone. Chem Phys Lett. 1993;216:362–8. Retrieved November 5, 2012. DOI: 10.1016/0009-2614(93)90110-M.Suche in Google Scholar

[9] Berry MV, Wilkinson M. Diabolical points in the spectra of triangles. Proc R Soc A Math, Phys Eng Sci. 1984;392:15–43. Retrieved October 26, 2012. http://rspa.royalsocietypublishing.org/cgi/doi/10.1098/rspa.1984.002210.1098/rspa.1984.0022Suche in Google Scholar

[10] Yarkony D. Diabolical conical intersections. Rev Mod Phys. 1996;68:985–1013.10.1103/RevModPhys.68.985Suche in Google Scholar

[11] Roos BO, Taylor PR, Siegbahn PEM. A complete active space SCF method (CASSCF) using a density matrix formulated super-CI approach. Chem Phys. 1980;48:157–73.10.1016/0301-0104(80)80045-0Suche in Google Scholar

[12] Foresman JB, Head-Gordon M, Pople JA, Frisch MJ. Toward a systematic molecular orbital theory for excited states. J Phys Chem. 1992;96:135–49.10.1021/j100180a030Suche in Google Scholar

[13] Trofimov AB, Krivdina IL, Weller J, Schirmer J. Algebraic-diagrammatic construction propagator approach to molecular response properties. Chem Phys. 2006;329:1–10.10.1016/j.chemphys.2006.07.015Suche in Google Scholar

[14] Schirmer J. Beyond the random-phase approximation: a new approximation scheme for the polarization propagator. Phys Rev. 1982;26:2395.10.1103/PhysRevA.26.2395Suche in Google Scholar

[15] Oddershede J. Propagator Methods. In: Advances in chemical physics. John Wiley & Sons, Inc, 2007:201–39.10.1002/9780470142943.ch3Suche in Google Scholar

[16] Christiansen O, Jørgensen P, Hättig C. Response functions from Fourier component variational perturbation theory applied to a time-averaged quasienergy. Int J Quantum Chem. 1998;68:1–52.10.1002/(SICI)1097-461X(1998)68:1<1::AID-QUA1>3.0.CO;2-ZSuche in Google Scholar

[17] Koch H, Jorgensen P. Coupled cluster response functions. J Chem Phys. 1990;93:3333–44.10.1063/1.458814Suche in Google Scholar

[18] Sekino H, Bartlett RJ. A linear response, coupled-cluster theory for excitation energy. Int J Quantum Chem. 1984;26:255–65.10.1002/qua.560260826Suche in Google Scholar

[19] Bauernschmitt R, Häser M, Treutler O, Ahlrichs R. Calculation of excitation energies within time-dependent density functional theory using auxiliary basis set expansions. Chem Phys Lett. 1997;264:573.10.1016/S0009-2614(96)01343-7Suche in Google Scholar

[20] Runge E, Gross EKU. Density-functional theory for time-dependent systems. Phys Rev Lett. 1984;52:997.10.1103/PhysRevLett.52.997Suche in Google Scholar

[21] Bartlett R, Musiał M. Coupled-cluster theory in quantum chemistry. Rev Mod Phys. 2007;79:291–352.10.1103/RevModPhys.79.291Suche in Google Scholar

[22] Koch H, Christiansen O, Jørgensen P, Olsen J. Excitation energies of BH, CH2 and Ne in full configuration interaction and the hierarchy CCS, CC2, CCSD and CC3 of coupled cluster models. Chem Phys Lett. 1995;244:75–82.10.1016/0009-2614(95)00914-PSuche in Google Scholar

[23] Hättig C, Weigend F. CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. J Chem Phys. 2000;113:5154.10.1063/1.1290013Suche in Google Scholar

[24] Christiansen O, Koch H, Jørgensen P. The second-order approximate coupled cluster singles and doubles model CC2. Chem Phys Lett. 1995b;243:409–18.10.1016/0009-2614(95)00841-QSuche in Google Scholar

[25] Christiansen O, Koch H, Jørgensen P. Response functions in the CC3 iterative triple excitation model. J Chem Phys. 1995a;103:7429–41.10.1063/1.470315Suche in Google Scholar

[26] Köhn A, Tajti A. Can coupled-cluster theory treat conical intersections?. J Chem Phys. 2007;127:044105.10.1063/1.2755681Suche in Google Scholar PubMed

[27] Kats D, Usvyat D, Schütz M. Second-order variational coupled-cluster linear-response method: a Hermitian time-dependent theory. Phys Rev. 2011;83:062503.10.1103/PhysRevA.83.062503Suche in Google Scholar

[28] Wälz G, Kats D, Usvyat D, Korona T, Schütz M. Application of Hermitian time-dependent coupled-cluster response Ansätze of second order to excitation energies and frequency-dependent dipole polarizabilities. Phys Rev. 2012;86:052519.10.1103/PhysRevA.86.052519Suche in Google Scholar

[29] Ledermüller K, Schütz M. Local CC2 response method based on the Laplace transform: analytic energy gradients for ground and excited states. J Chem Phys. 2014;140:164113.10.1063/1.4872169Suche in Google Scholar PubMed

[30] Kats D, Schütz M. A multistate local coupled cluster CC2 response method based on the Laplace transform. J Chem Phys. 2009;131:124117.10.1063/1.3237134Suche in Google Scholar PubMed

[31] Ledermüller K, Kats D, Schütz M. Local CC2 response method based on the Laplace transform: orbital-relaxed first-order properties for excited states. J Chem Phys. 2013;139:084111.10.1063/1.4818586Suche in Google Scholar PubMed

[32] Schütz M. Oscillator strengths, first-order properties, and nuclear gradients for local ADC (2). J Chem Phys. 2015;142:214103.10.1063/1.4921839Suche in Google Scholar PubMed

[33] Hohenberg P. Inhomogeneous electron gas. Phys Rev. 1964;136:B864–71.10.1103/PhysRev.136.B864Suche in Google Scholar

[34] Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys. 1993b;98:5648.10.1063/1.464913Suche in Google Scholar

[35] Casida ME, Huix-Rotllant M. Progress in time-dependent density-functional theory. Annu Rev Phys Chem. 2012;63:287–323.10.1146/annurev-physchem-032511-143803Suche in Google Scholar PubMed

[36] Parac M, Grimme S. Comparison of multireference Møller−Plesset theory and time-dependent methods for the calculation of vertical excitation energies of molecules. J Phys Chem. 2002;106:6844–50.10.1021/jp020550eSuche in Google Scholar

[37] Dreuw A, Weisman JL, Head-Gordon M. Long-range charge-transfer excited states in time-dependent density functional theory require non-local exchange. J Chem Phys. 2003;119:2943–7.10.1063/1.1590951Suche in Google Scholar

[38] Grimme S, Parac M. Substantial errors from time-dependent density functional theory for the calculation of excited states of large pi systems. Chemphyschem Eur J Chem Phys Phys Chem. 2003;4:292–5.10.1002/cphc.200390047Suche in Google Scholar PubMed

[39] Tozer D. Relationship between long-range charge-transfer excitation energy error and integer discontinuity in Kohn–Sham theory. J Chem Phys. 2003;119:12697–9.10.1063/1.1633756Suche in Google Scholar

[40] Peach MJG, Benfield P, Helgaker T, Tozer DJ. Excitation energies in density functional theory: an evaluation and a diagnostic test. J Chem Phys. 2008;128:44118.10.1063/1.2831900Suche in Google Scholar PubMed

[41] Yanai T, Tew DP, Handy NC. A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett. 2004;393:51–7.10.1016/j.cplett.2004.06.011Suche in Google Scholar

[42] Warshel A, Levitt M. Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilisation of the carbonium ion in the reaction of lysozyme. J Mol Biol. 1976;103:227–49.10.1016/0022-2836(76)90311-9Suche in Google Scholar PubMed

[43] Field MJ, Bash PA, Karplus M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem. 1990;11:700–33.10.1002/jcc.540110605Suche in Google Scholar

[44] Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–35.10.1063/1.445869Suche in Google Scholar

[45] Klamt A, Schuurmann G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans. 1993;2:799–805.10.1039/P29930000799Suche in Google Scholar

[46] Case DA, et al. The Amber biomolecular simulation programs. J Comput Chem. 2005;26:1668–88.10.1002/jcc.20290Suche in Google Scholar PubMed PubMed Central

[47] Brooks BR, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30:1545–614.10.1002/jcc.21287Suche in Google Scholar PubMed PubMed Central

[48] Brooks BR, et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4:187.10.1002/jcc.540040211Suche in Google Scholar

[49] Allinger NL, Kok RA, Imam MR. Hydrogen bonding in MM2. J Comput Chem. 1988;9:591–5.10.1002/jcc.540090602Suche in Google Scholar

[50] Allinger NL, Yuh YH, Lii JH. Molecular mechanics. The MM3 force field for hydrocarbons. 1. J Am Chem Soc. 1989;111:8551–66.10.1021/ja00205a001Suche in Google Scholar

[51] Allinger NL, Chen K, Lii JH. An improved force field (MM4) for saturated hydrocarbons. J Comput Chem. 1996;17:642–68.10.1002/(SICI)1096-987X(199604)17:5/6<642::AID-JCC6>3.0.CO;2-USuche in Google Scholar

[52] Rappe AK, Casewit CJ, Colwell KS, Goddard WA, Skiff WM. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc. 1992;114:10024–35.10.1021/ja00051a040Suche in Google Scholar

[53] Hess B, Kutzner C, Van Der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–47.10.1021/ct700301qSuche in Google Scholar

[54] Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–74.10.1002/jcc.20035Suche in Google Scholar

[55] Bayly CI, Cieplak P, Cornell W, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem. 1993;97:10269–80.10.1021/j100142a004Suche in Google Scholar

[56] Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. J Mol Structure: THEOCHEM. 2009;898:17–30.10.1016/j.theochem.2008.12.025Suche in Google Scholar

[57] Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res. 2010;43:142–51.10.1021/ar900171cSuche in Google Scholar

[58] Senn HM, Thiel W. QM/MM methods for biomolecular systems. Angew Chem Int Ed Engl. 2009;48:1198–229.10.1002/anie.200802019Suche in Google Scholar

[59] Hu LH, Söderhjelm P, Ryde U. On the convergence of QM/MM energies. J Chem Theory Comput. 2011;7:761–77.10.1021/ct100530rSuche in Google Scholar

[60] Mills G, Jónsson H. Quantum and thermal effects in H2 dissociative adsorption: evaluation of free energy barriers in multidimensional quantum systems. Phys Rev Lett. 1994;72:1124–7.10.1103/PhysRevLett.72.1124Suche in Google Scholar

[61] Sheppard D, Terrell R, Henkelman G. Optimization methods for finding minimum energy paths. J Chem Phys. 2008;128:134106.10.1063/1.2841941Suche in Google Scholar PubMed

[62] Klenin K, Strodel B, Wales DJ, Wenzel W. Modelling proteins: conformational sampling and reconstruction of folding kinetics. Biochim Biophys Acta. 2011;1814:977–1000.10.1016/j.bbapap.2010.09.006Suche in Google Scholar PubMed

[63] Lechner R, Kümmel S, König B. Visible light flavin photo-oxidation of methylbenzenes, styrenes and phenylacetic acids. Photochem Photobiol Sci: Off J Eur Photochem Assoc Eur Soc Photobiol. 2010;9: 1367–77.10.1039/c0pp00202jSuche in Google Scholar PubMed

[64] Megerle U, et al. Unraveling the flavin-catalyzed photooxidation of benzylic alcohol with transient absorption spectroscopy from sub-pico- to microseconds. Phys Chem Chem Phys. 2011;13:8869–80.10.1039/c1cp20190eSuche in Google Scholar PubMed

[65] Zheng Y-J, Ornstein RL. A theoretical study of the structures of flavin in different oxidation and protonation states. J Am Chem Soc. 1996;118:9402–8.10.1021/ja9608151Suche in Google Scholar

[66] Sikorska E, Khmelinskii IV, Koput J, Bourdelande JL, Sikorski M. Electronic structure of isoalloxazines in their ground and excited states. J Mol Struct. 2004;697:137–41.10.1016/j.molstruc.2004.04.005Suche in Google Scholar

[67] Salzmann S, Marian CM. The photophysics of alloxazine: a quantum chemical investigation in vacuum and solution. Photochem Photobiol Sci: Off J Eur Photochem Assoc Eur Soc Photobiol. 2009;8: 1655–66.10.1039/b9pp00022dSuche in Google Scholar PubMed

[68] Mathes T, Vogl C, Stolz J, Hegemann P. In vivo generation of flavoproteins with modified cofactors. J Mol Biol. 2009;385:1511–8.10.1016/j.jmb.2008.11.001Suche in Google Scholar PubMed

[69] Zirak P, Penzkofer A, Mathes T, Hegeman P. Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents. Chem Phys. 2009;358:111–22.10.1016/j.chemphys.2008.12.026Suche in Google Scholar

[70] Sadeghian K, Bocola M, Schütz M. A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors. J Am Chem Soc. 2008;130:12501–13.10.1021/ja803726aSuche in Google Scholar PubMed

[71] Sadeghian K, Bocola M, Schütz M. A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form. Phys Chem Chem Phys. 2010;12:8840–6.10.1039/b925908bSuche in Google Scholar PubMed

[72] Zirak P, Penzkofer A, Mathes T, Hegemann P. Absorption and emission spectroscopic characterization of BLUF protein Slr1694 from Synechocystis sp. PCC6803 with roseoflavin cofactor. J Photochem Photobiol B Biol. 2009;97:61–70.10.1016/j.jphotobiol.2009.08.002Suche in Google Scholar PubMed

[73] Merz T, Sadeghian K, Schütz M. Why BLUF photoreceptors with roseoflavin cofactor loose their biological functionality. Phys Chem Chem Phys. 2011;13:14775–83.10.1039/c1cp21386eSuche in Google Scholar PubMed

[74] Bauer A, Westkamper F, Grimme S, Bach T. Catalytic enantioselective reactions driven by photoinduced electron transfer. Nature. 2005;436:1139–40.10.1038/nature03955Suche in Google Scholar PubMed

[75] Fleming SA. Chemical reagents in photo affinity labeling. Tetrahedron. 1995;51:12479–520.10.1016/0040-4020(95)00598-3Suche in Google Scholar

[76] Ravelli D, Dondi D, Fagnoni M, Albini A. Photocatalysis. A multi-faceted concept for green chemistry. Chem Soc Rev. 2009;38:1999–2011.10.1039/b714786bSuche in Google Scholar PubMed

[77] Dorman G, Prestwich GD. Benzophenone photophores in biochemistry. Biochemistry. 1994;33:5661–73.10.1021/bi00185a001Suche in Google Scholar PubMed

[78] Galardy RE, Craig LC, Jamieson JD, Printz MP. Photoaffinity labeling of peptide hormone binding sites. J Biol Chem. 1974;249:3510–8.10.1016/S0021-9258(19)42601-XSuche in Google Scholar

[79] Cauble DF, Lynch V, Krische MJ. Studies on the enantioselective catalysis of photochemically promoted transformations: ‘sensitizing receptors’ as chiral catalysts. J Crganic Chem. 2003;68:15–21.10.1021/jo020630eSuche in Google Scholar PubMed

[80] Fagnoni M, Dondi D, Ravelli D, Albini A. Photocatalysis for the formation of the C-C bond. Chem Rev. 2007;107:2725–56. Retrieved October 26, 2012 http://www.ncbi.nlm.nih.gov/pubmed/17530909.10.1021/cr068352xSuche in Google Scholar PubMed

[81] Svoboda J, König B. Templated photochemistry: toward catalysts enhancing the efficiency and selectivity of photoreactions in homogeneous solutions. Chem Rev. 2006;106:5413–30.10.1021/cr050568wSuche in Google Scholar PubMed

[82] Müller C, et al. Enantioselective intramolecular [2 + 2]-photocycloaddition reactions of 4-substituted quinolones catalyzed by a chiral sensitizer with a hydrogen-bonding motif. J Am Chem Soc. 2011;133:16689–97.10.1021/ja207480qSuche in Google Scholar PubMed

[83] Wessig P. Organocatalytic enantioselective photoreactions. Angew Chem Int Ed Engl. 2006;45:2168–71.10.1002/anie.200503908Suche in Google Scholar PubMed

[84] Müller C, Bauer A, Bach T. Light-driven enantioselective organocatalysis. Angew Chem Int Ed Engl. 2009;48:6640–2.10.1002/anie.200901603Suche in Google Scholar PubMed

[85] Achenbach JC, Chiuman W, Cruz RPG, Li Y. DNAzymes: from creation in vitro to application in vivo. Curr Pharm Biotechnol. 2004;5:16.10.2174/1389201043376751Suche in Google Scholar PubMed

[86] Li Y, Breaker RR. Deoxyribozymes: new players in the ancient game of biocatalysis. Curr Opin Struct Biol. 1999;9:315–23.10.1016/S0959-440X(99)80042-6Suche in Google Scholar PubMed

[87] Babii O, et al. Direct photocontrol of peptidomimetics: an alternative to oxygen‐dependent photodynamic cancer therapy. Angewandte Chemie. 2016;128:5583–6.10.1002/ange.201600506Suche in Google Scholar

[88] Göstl R, Hecht S. Controlling covalent connection and disconnection with light. Angew Chem Int Ed. 2014;53:8784–7.10.1002/anie.201310626Suche in Google Scholar PubMed

[89] Göstl R, Hecht S. Photoreversible prodrugs and protags: switching the release of maleimides by using light under physiological conditions. Chem A Eur J. 2015;21:4422–7.10.1002/chem.201405767Suche in Google Scholar PubMed

[90] Grabowski ZR, Rotkiewicz K, Rettig W. Structural changes accompanying intramolecular electron transfer: focus on twisted intramolecular charge-transfer states and structures. Chem Rev. 2003;103:3899–4032.10.1021/cr940745lSuche in Google Scholar PubMed

[91] Yoshihara T, Druzhinin SI, Zachariasse KA. Fast intramolecular charge transfer with a planar rigidized electron donor/acceptor molecule. J Am Chem Soc. 2004;126:8535–9.10.1021/ja049809sSuche in Google Scholar PubMed

[92] Jung A, et al. Structure of a bacterial BLUF photoreceptor: insights into blue-mediated signal transduction. Proc Nat Acad Sci. 2005;101:12306–11.10.1073/pnas.0500722102Suche in Google Scholar PubMed PubMed Central

[93] Woon DE, Dunning Jr TH. Gaussian basis sets for use in correlated molecular calculations. III. The second row atoms, Al-Ar. J Chem Phys. 1993;98:1358–71.10.1063/1.464303Suche in Google Scholar

[94] Perdew J. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B. 1986;33:8822–4.10.1103/PhysRevB.33.8822Suche in Google Scholar PubMed

[95] Becke AD. A new mixing of Hartree–Fock and local density-functional theories. J Chem Phys. 1993a;98:1372.10.1063/1.464304Suche in Google Scholar

[96] Schäfer A, Horn H, Ahlrichs R. Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J Chem Phys. 1992;97:2571–8.10.1063/1.463096Suche in Google Scholar

[97] Grimme S, Waletzke M. A combination of Kohn–Sham density functional theory and multi-reference configuration interaction methods. J Chem Phys. 1999;111:5645–55.10.1063/1.479866Suche in Google Scholar

[98] Cremer D. On the correct usage of the Cremer–Pople puckering parameters as quantitative descriptors of ring shapes – a reply to recent criticism by Petit, Dillen and Geise. Acta Crystallogr B Struct Sci. 1984;40:498–500.10.1107/S0108768184002548Suche in Google Scholar