Year 2025,
Volume: 11 Issue: 1, 82 - 94, 31.03.2025
Fehime Hayal Geçit
,
Zühra Güneş
,
Murat Ertürk
,
Hüseyin Aksu
Project Number
Tübitak 1001 123Z591
References
- K. M. Kadish, K. M. Smith, R. Guilard, The porphyrin handbook: Inorganic, organometallic and coordination chemistry, Elsevier, 2000.
- D. Holten, D. F. Bocian, J. S. Lindsey, Probing electronic communication in covalently linked multi porphyrin arrays. A guide to the rational design of molecular photonic devices, Accounts of Chemical Research 35 (2002) 57–69.
- K. M. Kadish, Porphyrin science: With applications to chemistry, physics, materials science, engineering, biology and medicine, World Scientific, 2010.
- E. Yang, C. Kirmaier, M. Krayer, M. Taniguchi, H.-J. Kim, J. R. Diers, D. F. Bocian, J. S. Lindsey, D. Holten, Photophysical properties and electronic structure of stable, tunable synthetic bacteriochlorins: Extending the features of native photosynthetic pigments, The Journal of Physical Chemistry B 115 (37) (2011) 10801–10816.
- M. Gouterman, G. H. Wagnière, L. C. Snyder, Spectra of porphyrins: Part II. Four orbital model, Journal of Molecular Spectroscopy 11 (1-6) (1963) 108–127.
- S. Fukuzumi, K. Ohkubo, X. Zheng, Y. Chen, R. K. Pandey, R. Zhan, K. M. Kadish, Metal bacteriochlorins which act as dual singlet oxygen and superoxide generators, The Journal of Physical Chemistry B 112 (9) (2008) 2738–2746.
- T. Miyatake, H. Tamiaki, A. R. Holzwarth, K. Schaffner, Artificial light-harvesting antennae: Singlet excitation energy transfer from zinc chlorin aggregate to bacteriochlorin in homogeneous hexane solution, Photochemistry and Photobiology 69 (4) (1999) 448–456.
- M. R. Wasielewski, W. A. Svec, Synthesis of covalently linked dimeric derivatives of chlorophyll a, pyrochlorophyll a, chlorophyll b, and bacteriochlorophyll a, The Journal of Organic Chemistry 45 (10) (1980) 1969–1974.
- J. S. Lindsey, O. Mass, C. -Y. Chen, Tapping the near-infrared spectral region with bacteriochlorin arrays, New Journal of Chemistry 35 (3) (2011) 511–516.
- A. N. Kozyrev, Y. Chen, L. N. Goswami, W. A. Tabaczynski, R. K. Pandey, Characterization of porphyrins, chlorins, and bacteriochlorins formed via allomerization of bacteriochlorophyll a. Synthesis of highly stable bacteriopurpurinimides and their metal complexes, The Journal of Organic Chemistry 71 (5) (2006) 1949–1960.
- C. McCleese, Z. Yu, N. N. Esemoto, C. Kolodziej, B. Maiti, S. Bhandari, B. D. Dunietz, C. Burda, M. Ptaszek, Excitonic interactions in bacteriochlorin homo-dyads enable charge transfer: A new approach to the artificial photosynthetic special pair, The Journal of Physical Chemistry B 122 (14) (2018) 4131–4140.
- E. Yang, J. Wang, J. R. Diers, D. M. Niedzwiedzki, C. Kirmaier, D. F. Bocian, J. S. Lindsey, D. Holten, Probing electronic communication for efficient light-harvesting functionality: Dyads containing a common perylene and a porphyrin, chlorin, or bacteriochlorin, The Journal of Physical Chemistry B 118 (6) (2014) 1630–1647.
- H. Aksu, B. Maiti, M. Ptaszek, B. D. Dunietz, Photoinduced charge transfer in Zn(II) and Au(III)-ligated symmetric and asymmetric bacteriochlorin dyads: A computational study, The Journal of Chemical Physics 153 (13) (2020) 134111.
- R. E. Blankenship, Molecular mechanisms of photosynthesis, John Wiley and Sons, 2014.
- P. Hepworth, J. McCombie, J. Simons, J. Pfanstiel, J. Ribblett, D. Pratt, High-resolution electronic spectroscopy of molecular conformers. 3-Hydroxy and 3-deuteroxy benzoic acid esters, Chemical Physics Letters 236 (6) (1995) 571-–579.
- R. T. Kroemer, K. R. Liedl, J. A. Dickinson, E. G. Robertson, J. P. Simons, D. R. Borst, D. W. Pratt, Conformationally induced changes in the electronic structures of some flexible benzenes. A molecular orbital model, The American Chemical Society 120 (1998) 12573–12582.
- P. Hepworth, J. McCombie, J. Simons, J. Pfanstiel, J. Ribblett, D. Pratt, High resolution electronic spectroscopy of molecular conformers. Methyl- and ethyl-3-aminobenzoic acid esters, Chemical Physics Letters 249 (5-6) (1996) 341350.
- J. A. Dickinson, M. R. Hockridge, R. T. Kroemer, E. G. Robertson, J. P. Simons, J. McCombie, M. Walker, Conformational choice, hydrogen bonding, and rotation of the S1←S0 electronic transition moment in 2-phenylethyl alcohol, 2-phenylethylamine, and their water clusters, The American Chemical Society 120 (11) (1998) 2622–2632.
- M. R. Hockridge, S. M. Knight, E. G. Robertson, J. P. Simons, J. McCombie, M. Walker, Conformational landscapes in flexible organic molecules: 4-hydroxy phenyl ethanol (p-tyrosol) and its singly hydrated complex, Physical Chemistry Chemical Physics 1 (1999) 407–413.
- C. Brand, W. L. Meerts, M. Schmitt, How and why do transition dipole moment orientations depend on conformer structure?, The Journal of Physical Chemistry A 115 (34) (2011) 9612–9619.
- H. Aksu, A. Schubert, E. Geva, B. D. Dunietz, Explaining spectral asymmetries and excitonic characters of the core pigment pairs in the bacterial reaction center using screened range-separated hybrid functionals, The Journal of Physical Chemistry B 123 (42) (2019) 8970–8975.
- H. Aksu, A. Schubert, S. Bhandari, A. Yamada, E. Geva, B. D. Dunietz, On the role of the special pair in photosynthesis as a charge transfer rectifier, The Journal of Physical Chemistry B 124 (10) (2020) 1987–1994.
- P. Hohenberg, W. Kohn, Inhomogeneous electron gas, Physical Review B 136 (1964) B864.
- J. Tomasi, B. Mennucci, R. Cammi, Quantum mechanical continuum solvation models, Chemical Review 105 (5) (2005) 2999–3094.
- A. W. Lange, J. M. Herbert, Polarizable continuum reaction-field solvation models affording smooth potential energy surfaces, The Journal of Physical Chemistry Letters 1 (2) (2009) 556–561.
- S. Bhandari, M. S. Cheung, E. Geva, L. Kronik, B. D. Dunietz, Fundamental gaps of condensed-phase organic semiconductors from single-molecule calculations using polarization-consistent optimally tuned screened range-separated hybrid functionals, The Journal of Chemical Theory and Computation 14 (12) (2018) 6287–6294.
- E. Runge, E. K. Gross, Density-functional theory for time-dependent systems, Physical Review Letters 52 (1984) 997.
- J. D. Chai, M. Head-Gordon, Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections, Physical Chemistry Chemical Physics 10 (44) (2008) 6615–6620.
- R. Ditchfield, W. J. Hehre, J. A. Pople, Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules, Journal of Chemical Physics 54 (2) (1971) 724–728.
- Y. Shao, et al., Advances in methods and algorithms in a modern quantum chemistry program package, Physical Chemistry Chemical Physics 8 (27) (2006) 3172–3191.
- N. Kuritz, T. Stein, R. Baer, L. Kronik, Charge-transfer-like $\pi-\pi^*$ excitations in time-dependent density functional theory: A conundrum and its solution, The Journal of Chemical Theory and Computation 7 (8) (2011) 2408–2415.
- Z. Zheng, D. A. Egger, J. -L. Bredas, L. Kronik, V. Coropceanu, Effect of solid-state polarization on charge-transfer excitations and transport levels at organic interfaces from a screened rangeseparated hybrid functional, The Journal of Physical Chemistry Letter 8 (14) (2017) 3277–3283.
- L. Kronik, S. Kümmel, Dielectric screening meets optimally tuned density functionals, Advanced Materials 30 (41) (2018) 1–14.
- S. Refaely-Abramson, M. Jain, S. Sharifzadeh, J. B. Neaton, L. Kronik, Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory, Physical Review B 92 (2015) 081204.
- M. Kasha, H. Rawls, M. Ashraf El-Bayoumi, The exciton model in molecular spectroscopy, the journal Pure and Applied Chemistry 11 (3-4) (1965) 371–392.
- U. Ermler, G. Fritzsch, S. K. Buchanan, H. Michel, Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: Cofactors and protein-cofactor interactions, Structure 2 (10) (1994) 925–936.
- M. A. Rohrdanz, K. M. Martins, J. M. Herbert, A Long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states, The Journal of Chemical Physics 130 (5) (2009) 054112.
- B. Joo, H. Han, E.-G. Kim, Solvation-mediated tuning of the range-separated hybrid functional:Self-sufficiency through screened exchange, The Journal of Chemical Theory and Computation 14 (6) (2018) 2823–2828.
- Y. Song, A. Schubert, E. Maret, R. K. Burdick, B. D. Dunietz, E. Geva, J. P. Ogilvie, Vibronic structure of photosynthetic pigments probed by polarized two-dimensional electronic spectroscopy and ab initio calculations, Chemical Science 10 (2019) 8143.
- K. Begam, H. Aksu, B. D. Dunietz, Antioxidative Triplet excitation energy transfer in bacterial reaction center using a screened range separated hybrid functional, The Journal of Physical Chemistry B 128 (18) (2024) 4315–4324.
- C. Chakravarty, M. A. C. Saller, H. Aksu, B. D. Dunietz, Anisotropic dielectric screened range-separated hybrid density functional theory calculations of charge transfer states in Anthracene-TCNQ donor-acceptor complex, The Journal of Chemical Theory and Computation 20 (24) (2024) 10751–10758.
- C. Chakravarty, H. Aksu, B. Martinez P. Ramos, M. Pavanello, B. D. Dunietz, Role of dielectric screening in calculating excited states of solvated azobenzene: A benchmark study comparing quantum embedding and polarizable Continuum Model for Representing the Solvent, The Journal of Physical Chemistry Letters 13 (22) (2022) 4849.
- T. Stein, L. Kronik, R. Baer, Prediction of charge-transfer excitations in coumarin-based dyes using a range-separated functional tuned from first principles, Journal of Chemical Physics 131 (24) (2009) 244119.
The Role of Polar Functional Groups of the Special Pair on the Excites States in Terms of the Dielectric Environment: Screened Range Separated Time-Dependent Density Functional Theory
Year 2025,
Volume: 11 Issue: 1, 82 - 94, 31.03.2025
Fehime Hayal Geçit
,
Zühra Güneş
,
Murat Ertürk
,
Hüseyin Aksu
Abstract
We study the role of polar functional groups (PFGs) on the excited states and the changes of net charges on the charge transfer (CT) states in terms of dielectric constant using ab initio theory. It is found that the PFGs play a dielectric medium in which the side PFGs interact strongly with the incoming light, and this interaction contributes to the wave function of excited states. Results reveal that conformer structure due to side groups has more influence on transition dipole moment (TDM) and thus on the electronic excitations. We have also discussed the well-known J- and H- aggregation physical phenomenon for the special pair and shown the excitonic splitting energies of the special pair compared to the monomer's first excited state energies. Excitation energies, oscillator strength, and CT states are obtained by using time-dependent density functional theory (TDDFT) and accompanying screened range-separated hybrid functionals (SRSH) in which comparisons are made with $\omega$B97X-D functional.
Ethical Statement
No approval from the Board of Ethics is required.
Supporting Institution
Çanakkale Onsekiz Mart University
Project Number
Tübitak 1001 123Z591
Thanks
This study was supported by the Scientific and Technological Research Council of Türkiye (TUBITAK), Grant Number 123Z591 (TUBITAK 1001).
References
- K. M. Kadish, K. M. Smith, R. Guilard, The porphyrin handbook: Inorganic, organometallic and coordination chemistry, Elsevier, 2000.
- D. Holten, D. F. Bocian, J. S. Lindsey, Probing electronic communication in covalently linked multi porphyrin arrays. A guide to the rational design of molecular photonic devices, Accounts of Chemical Research 35 (2002) 57–69.
- K. M. Kadish, Porphyrin science: With applications to chemistry, physics, materials science, engineering, biology and medicine, World Scientific, 2010.
- E. Yang, C. Kirmaier, M. Krayer, M. Taniguchi, H.-J. Kim, J. R. Diers, D. F. Bocian, J. S. Lindsey, D. Holten, Photophysical properties and electronic structure of stable, tunable synthetic bacteriochlorins: Extending the features of native photosynthetic pigments, The Journal of Physical Chemistry B 115 (37) (2011) 10801–10816.
- M. Gouterman, G. H. Wagnière, L. C. Snyder, Spectra of porphyrins: Part II. Four orbital model, Journal of Molecular Spectroscopy 11 (1-6) (1963) 108–127.
- S. Fukuzumi, K. Ohkubo, X. Zheng, Y. Chen, R. K. Pandey, R. Zhan, K. M. Kadish, Metal bacteriochlorins which act as dual singlet oxygen and superoxide generators, The Journal of Physical Chemistry B 112 (9) (2008) 2738–2746.
- T. Miyatake, H. Tamiaki, A. R. Holzwarth, K. Schaffner, Artificial light-harvesting antennae: Singlet excitation energy transfer from zinc chlorin aggregate to bacteriochlorin in homogeneous hexane solution, Photochemistry and Photobiology 69 (4) (1999) 448–456.
- M. R. Wasielewski, W. A. Svec, Synthesis of covalently linked dimeric derivatives of chlorophyll a, pyrochlorophyll a, chlorophyll b, and bacteriochlorophyll a, The Journal of Organic Chemistry 45 (10) (1980) 1969–1974.
- J. S. Lindsey, O. Mass, C. -Y. Chen, Tapping the near-infrared spectral region with bacteriochlorin arrays, New Journal of Chemistry 35 (3) (2011) 511–516.
- A. N. Kozyrev, Y. Chen, L. N. Goswami, W. A. Tabaczynski, R. K. Pandey, Characterization of porphyrins, chlorins, and bacteriochlorins formed via allomerization of bacteriochlorophyll a. Synthesis of highly stable bacteriopurpurinimides and their metal complexes, The Journal of Organic Chemistry 71 (5) (2006) 1949–1960.
- C. McCleese, Z. Yu, N. N. Esemoto, C. Kolodziej, B. Maiti, S. Bhandari, B. D. Dunietz, C. Burda, M. Ptaszek, Excitonic interactions in bacteriochlorin homo-dyads enable charge transfer: A new approach to the artificial photosynthetic special pair, The Journal of Physical Chemistry B 122 (14) (2018) 4131–4140.
- E. Yang, J. Wang, J. R. Diers, D. M. Niedzwiedzki, C. Kirmaier, D. F. Bocian, J. S. Lindsey, D. Holten, Probing electronic communication for efficient light-harvesting functionality: Dyads containing a common perylene and a porphyrin, chlorin, or bacteriochlorin, The Journal of Physical Chemistry B 118 (6) (2014) 1630–1647.
- H. Aksu, B. Maiti, M. Ptaszek, B. D. Dunietz, Photoinduced charge transfer in Zn(II) and Au(III)-ligated symmetric and asymmetric bacteriochlorin dyads: A computational study, The Journal of Chemical Physics 153 (13) (2020) 134111.
- R. E. Blankenship, Molecular mechanisms of photosynthesis, John Wiley and Sons, 2014.
- P. Hepworth, J. McCombie, J. Simons, J. Pfanstiel, J. Ribblett, D. Pratt, High-resolution electronic spectroscopy of molecular conformers. 3-Hydroxy and 3-deuteroxy benzoic acid esters, Chemical Physics Letters 236 (6) (1995) 571-–579.
- R. T. Kroemer, K. R. Liedl, J. A. Dickinson, E. G. Robertson, J. P. Simons, D. R. Borst, D. W. Pratt, Conformationally induced changes in the electronic structures of some flexible benzenes. A molecular orbital model, The American Chemical Society 120 (1998) 12573–12582.
- P. Hepworth, J. McCombie, J. Simons, J. Pfanstiel, J. Ribblett, D. Pratt, High resolution electronic spectroscopy of molecular conformers. Methyl- and ethyl-3-aminobenzoic acid esters, Chemical Physics Letters 249 (5-6) (1996) 341350.
- J. A. Dickinson, M. R. Hockridge, R. T. Kroemer, E. G. Robertson, J. P. Simons, J. McCombie, M. Walker, Conformational choice, hydrogen bonding, and rotation of the S1←S0 electronic transition moment in 2-phenylethyl alcohol, 2-phenylethylamine, and their water clusters, The American Chemical Society 120 (11) (1998) 2622–2632.
- M. R. Hockridge, S. M. Knight, E. G. Robertson, J. P. Simons, J. McCombie, M. Walker, Conformational landscapes in flexible organic molecules: 4-hydroxy phenyl ethanol (p-tyrosol) and its singly hydrated complex, Physical Chemistry Chemical Physics 1 (1999) 407–413.
- C. Brand, W. L. Meerts, M. Schmitt, How and why do transition dipole moment orientations depend on conformer structure?, The Journal of Physical Chemistry A 115 (34) (2011) 9612–9619.
- H. Aksu, A. Schubert, E. Geva, B. D. Dunietz, Explaining spectral asymmetries and excitonic characters of the core pigment pairs in the bacterial reaction center using screened range-separated hybrid functionals, The Journal of Physical Chemistry B 123 (42) (2019) 8970–8975.
- H. Aksu, A. Schubert, S. Bhandari, A. Yamada, E. Geva, B. D. Dunietz, On the role of the special pair in photosynthesis as a charge transfer rectifier, The Journal of Physical Chemistry B 124 (10) (2020) 1987–1994.
- P. Hohenberg, W. Kohn, Inhomogeneous electron gas, Physical Review B 136 (1964) B864.
- J. Tomasi, B. Mennucci, R. Cammi, Quantum mechanical continuum solvation models, Chemical Review 105 (5) (2005) 2999–3094.
- A. W. Lange, J. M. Herbert, Polarizable continuum reaction-field solvation models affording smooth potential energy surfaces, The Journal of Physical Chemistry Letters 1 (2) (2009) 556–561.
- S. Bhandari, M. S. Cheung, E. Geva, L. Kronik, B. D. Dunietz, Fundamental gaps of condensed-phase organic semiconductors from single-molecule calculations using polarization-consistent optimally tuned screened range-separated hybrid functionals, The Journal of Chemical Theory and Computation 14 (12) (2018) 6287–6294.
- E. Runge, E. K. Gross, Density-functional theory for time-dependent systems, Physical Review Letters 52 (1984) 997.
- J. D. Chai, M. Head-Gordon, Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections, Physical Chemistry Chemical Physics 10 (44) (2008) 6615–6620.
- R. Ditchfield, W. J. Hehre, J. A. Pople, Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules, Journal of Chemical Physics 54 (2) (1971) 724–728.
- Y. Shao, et al., Advances in methods and algorithms in a modern quantum chemistry program package, Physical Chemistry Chemical Physics 8 (27) (2006) 3172–3191.
- N. Kuritz, T. Stein, R. Baer, L. Kronik, Charge-transfer-like $\pi-\pi^*$ excitations in time-dependent density functional theory: A conundrum and its solution, The Journal of Chemical Theory and Computation 7 (8) (2011) 2408–2415.
- Z. Zheng, D. A. Egger, J. -L. Bredas, L. Kronik, V. Coropceanu, Effect of solid-state polarization on charge-transfer excitations and transport levels at organic interfaces from a screened rangeseparated hybrid functional, The Journal of Physical Chemistry Letter 8 (14) (2017) 3277–3283.
- L. Kronik, S. Kümmel, Dielectric screening meets optimally tuned density functionals, Advanced Materials 30 (41) (2018) 1–14.
- S. Refaely-Abramson, M. Jain, S. Sharifzadeh, J. B. Neaton, L. Kronik, Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory, Physical Review B 92 (2015) 081204.
- M. Kasha, H. Rawls, M. Ashraf El-Bayoumi, The exciton model in molecular spectroscopy, the journal Pure and Applied Chemistry 11 (3-4) (1965) 371–392.
- U. Ermler, G. Fritzsch, S. K. Buchanan, H. Michel, Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: Cofactors and protein-cofactor interactions, Structure 2 (10) (1994) 925–936.
- M. A. Rohrdanz, K. M. Martins, J. M. Herbert, A Long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states, The Journal of Chemical Physics 130 (5) (2009) 054112.
- B. Joo, H. Han, E.-G. Kim, Solvation-mediated tuning of the range-separated hybrid functional:Self-sufficiency through screened exchange, The Journal of Chemical Theory and Computation 14 (6) (2018) 2823–2828.
- Y. Song, A. Schubert, E. Maret, R. K. Burdick, B. D. Dunietz, E. Geva, J. P. Ogilvie, Vibronic structure of photosynthetic pigments probed by polarized two-dimensional electronic spectroscopy and ab initio calculations, Chemical Science 10 (2019) 8143.
- K. Begam, H. Aksu, B. D. Dunietz, Antioxidative Triplet excitation energy transfer in bacterial reaction center using a screened range separated hybrid functional, The Journal of Physical Chemistry B 128 (18) (2024) 4315–4324.
- C. Chakravarty, M. A. C. Saller, H. Aksu, B. D. Dunietz, Anisotropic dielectric screened range-separated hybrid density functional theory calculations of charge transfer states in Anthracene-TCNQ donor-acceptor complex, The Journal of Chemical Theory and Computation 20 (24) (2024) 10751–10758.
- C. Chakravarty, H. Aksu, B. Martinez P. Ramos, M. Pavanello, B. D. Dunietz, Role of dielectric screening in calculating excited states of solvated azobenzene: A benchmark study comparing quantum embedding and polarizable Continuum Model for Representing the Solvent, The Journal of Physical Chemistry Letters 13 (22) (2022) 4849.
- T. Stein, L. Kronik, R. Baer, Prediction of charge-transfer excitations in coumarin-based dyes using a range-separated functional tuned from first principles, Journal of Chemical Physics 131 (24) (2009) 244119.