Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study... more Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study of resonance energy transfer (RET). However, most of these calculations rely on approximate QM methods due to the computational limitations imposed by the size of typical donor-acceptor systems. In this work, we present a novel implementation that allows computing electronic couplings at the coupled cluster singles and doubles (CCSD) level of theory. Solvent effects are also taken into account through the polarizable continuum model (PCM). As a test case, we use a dimer of indole, a common model system for tryptophan, which is routinely used as an intrinsic fluorophore in Förster resonance energy transfer studies. We consider two bright π → π* states, one of which has charge transfer character. Lastly, the results are compared with those obtained by applying TD-DFT in combination with one of the most popular density functionals, B3LYP.
The nature of the coupling of the photoexcited chromophore with the environment in a prototypical... more The nature of the coupling of the photoexcited chromophore with the environment in a prototypical system like green fluorescent protein (GFP) is to date not understood, and its description still defies state-of-the-art multiscale approaches. To identify which theoretical framework of the chromophore-protein complex can realistically capture its essence, we employ here a variety of electronic-structure methods, namely, time-dependent density functional theory (TD-DFT), multireference perturbation theory (NEVPT2 and CASPT2), and quantum Monte Carlo (QMC) in combination with static point charges (QM/MM), DFT embedding (QM/DFT), and classical polarizable embedding through induced dipoles (QM/MMpol). Since structural modifications can significantly affect the photophysics of GFP, we also account for thermal fluctuations through extensive molecular dynamics simulations. We find that a treatment of the protein through static point charges leads to significantly blue-shifted excitation energies and that including thermal fluctuations does not cure the coarseness of the MM description. While TDDFT calculations on large cluster models indicate the need of a responsive protein, this response is not simply electrostatic: An improved description of the protein in the ground state or in response to the excitation of the chromophore via ground-state or state-specific DFT and MMpol embedding does not significantly modify the results obtained with static point charges. Through the use of QM/MMpol in a linear response formulation, a different picture in fact emerges in which the main environment response to the chromophore excitation is the one coupling the transition density and the corresponding induced dipoles. Such interaction leads to significant red-shifts and a satisfactory agreement with full QM cluster calculations at the same level of theory. Our findings demonstrate that, ultimately, faithfully capturing the effects of the environment in GFP requires a quantum treatment of large photoexcited regions but that a QM/classical model can be a useful approximation when extended beyond the electrostatic-only formulation.
In the last decade, much progress has been made in the understanding of DNA excited-state dynamic... more In the last decade, much progress has been made in the understanding of DNA excited-state dynamics. In this context, theoretical studies focused both on the photophysical properties of individual nucleobases as well as on the relevant interactions in assemblies of two or more bases have been a valuable tool for exploring decay mechanisms of excited states in DNA. In contrast to singlet excited states, our knowledge on the energetics and dynamics of triplet excited states is still largely limited to the properties of individual bases. Thus, despite the fact that triplet-triplet electronic energy transfer (TET) can initiate phototoxic reactions in DNA, such as the formation of thymine cyclobutane dimers, little is known about the strength of the electronic interactions and the timescales for TET in nucleobase p stacks: the factors that determine the fate of triplet states in native DNA. Therefore, the assignment of decay components measured through ultrafast spectroscopy experiments remains a difficult task owing to the fundamental uncertainty regarding the degree of delocalization of triplet excited states and the approximate timescales for their migration. Herein, we present a study of TET between stacked adenine-adenine (A-A) and tymine-thymine (T-T) in polyA-polyT DNA sequences. We applied the semiempirical ZINDO method to investigate how DNA structural dynamics modulate the couplings for TET along a 15 ns classical molecular-dynamics (MD) trajectory. The suitability of the ZINDO method for describing the energetics and TET couplings of low-lying p!p* triplet states was validated by comparison with equation-of-motion coupled-cluster models with single and double substitutions (EOM-CCSD) and
This contribution presents a detalied theoretical study on how proteins regulate the electronic c... more This contribution presents a detalied theoretical study on how proteins regulate the electronic couplings responsible for exciton delocalization and electronic energy transfer (EET) in photosynthetic pigmentprotein complexes. Understanding environment effects, which cause line broadening and screen electronic interactions, is fundamentally important because of its central role in the control of EET dynamics. Recent work has furthermore shown that simple models for solvation may not be sufficient to explain effects that go beyond Förster theory, such as coherent contribution to energy transfer. Here, we focus on the phycobiliprotein PE545 from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24,3 and apply a novel combined quantum mechanics/molecular mechanics (QM/MM) method4 that explicitly incorporates environment polarization (protein and solvent) at the atomic level on the calculation of site energies and electronic couplings, thus going beyond the continuum dielectr...
We present the formulation and implementation of a polarizable quantum mechanics/molecular mechan... more We present the formulation and implementation of a polarizable quantum mechanics/molecular mechanics (QM/MM) strategy to describe environment effects in multiconfiguration self-consistent field calculations. The strategy is applied to the calculation of the vertical absorption spectrum of cytosine in water. In our approach, mutual polarization of the solute and the solvent is solved self-consistently at the complete-active-space self-consistent-field (CASSCF) level, and the resulting set of charges and dipoles is used to calculate vertical excitation energies using the complete-active-space second-order perturbative (CASPT2) approach and its multistate (MS-CASPT2) variant. In order to treat multiple excited states, we converge the solvent polarization with respect to the state-averaged density of the solute. In order to obtain the final energies, however, we introduce a state-specific correction, where the solvent polarization is recomputed with the density of each state, and demonstrate that this correction brings the excitation energies closer to the values obtained with state-optimized orbitals. Comparison with PCM and nonpolarizable QM/MM calculations shows the importance of specific solute-solvent interactions and environment polarization in describing experiments. Overall, the calculated excitations for the π → π* states in water show good agreement with the experimental spectrum, whereas the n → π* appear at energies above 6 eV, approximately 1 eV higher than in the gas phase. Beyond solvents, the new method will allow studying the impact of heterogeneous biological environments in multiple excited states, as well as the treatment of multichromophoric systems where charge transfer and exciton states play important roles.
Electronic energy transfer is reviewed with a particular emphasis on its role in photosynthesis. ... more Electronic energy transfer is reviewed with a particular emphasis on its role in photosynthesis. The article describes the advances in theory that have been motivated by studies of photosynthetic light harvesting antenna proteins. Noting that most theoretical work presently focuses on just a few photosynthetic systems, the extraordinary scope and diversity of systems actually found in nature is described.
Advances in electronic spectroscopies with femtosecond time resolution have provided new informat... more Advances in electronic spectroscopies with femtosecond time resolution have provided new information on the excitonic processes taking place during the energy conversion in natural photosynthetic antennae. This has promoted the development of new theoretical protocols aiming at accurately describing the properties and mechanisms of exciton formation and relaxation. In this perspective, we provide an overview of the quantum chemical based approaches, trying to underline both the potentials of the methods and their weaknesses. In particular three main aspects will be analysed, the quantum mechanical description of excitonic parameters (site energies and couplings), the incorporation of environmental effects on these parameters through hybrid quantum/classical approaches, and the modelling of the dynamical coupling among such parameters and the vibrations of the pigment-protein complex.
An extension of the Miertus-Scrocco-Tomasi (MST) continuum method to the Integral Equation Formal... more An extension of the Miertus-Scrocco-Tomasi (MST) continuum method to the Integral Equation Formalism (IEF) is presented. In particular, we report here the parametrization of the MST(IEF) model to the solvation in water, octanol, chloroform and carbon tetrachloride. A detailed comparison is made between the results obtained from the MST(PCM) formalism corrected by using diverse charge normalization schemes and those obtained from the IEF formalism. The IEF method is found to provide results in close agreement with those obtained within the PCM framework by taking into account the anisotropy of the solute's charge distribution in the charge normalization of the apparent surface charge that simulates the solvent reaction field. Besides the standard HF/6-31G(d) level of theory considered in previous parametrizations of the MST(PCM) model, we also report here the results obtained for the B3LYP hybrid density functional method. These results indicate that there are small differences in the electrostatic component of the solvation free energy determined from HF and B3LYP levels of theory, which might be captured by suitable adjustment of the atomic surface tensions in the van der Waals component. Overall, the results support the strategy used in the development of the MST model and its suitability as a robust approach to the study of molecules in solution. q
ABSTRACT A combined molecular dynamics and a polarizable quantum mechanics (QM)/molecular mechani... more ABSTRACT A combined molecular dynamics and a polarizable quantum mechanics (QM)/molecular mechanics (MM) approach can be used to obtain a reliable picture of the excitonic properties of the Fenna–Matthews–Olson (FMO) protein, as shown on p. 3194, by B. Mennucci et al.
Excitation energy transfer involving semiconductor quantum dots (QDs) has received increased atte... more Excitation energy transfer involving semiconductor quantum dots (QDs) has received increased attention in recent years because their properties, such as high photostability and size-tunable optical properties, have made QDs attractive as F rster resonant energy transfer (FRET) ...
Long-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low... more Long-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low and at room temperatures have generated a heated debate over the impact that the coupling of electronic excitations to molecular vibrations of the relevant actors (pigments, proteins and solvents) has on the excitation energy transfer process. In this work, we use a combined MD and QM/MMPol strategy to investigate the exciton-phonon interactions in the PE545 light-harvesting complex by computing the spectral densities for each pigment and analyzing their consequences in the exciton dynamics. Insights into the origin of relevant peaks, as well as their differences among individual pigments, are provided by correlating them with normal modes obtained from a quasi-harmonic analysis of the motions sampled by the pigments in the complex. Our results indicate that both the protein and the solvent significantly modulate the intramolecular vibrations of the pigments thus playing an important role in promoting or suppressing certain exciton-phonon interactions. We also find that these low-frequency features are largely smoothed out when the spectral density is averaged over the complex, something difficult to avoid in experiments that underscores the need to combine theory and experiment to understand the origin of quantum coherence in photosynthetic light-harvesting.
International Conference on Ultrafast Phenomena, 2010
Page 1. Quantum-Coherent Energy Transfer in Marine Algae at Ambient Temperature via Ultrafast Pho... more Page 1. Quantum-Coherent Energy Transfer in Marine Algae at Ambient Temperature via Ultrafast Photon Echo Studies Cathy Y. Wong, Hoda Hossein-Nejad, Carles Curutchet and Gregory D. Scholes* Department of Chemistry, 80 St. ...
We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analy... more We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.
We present a quantum-mechanical study of excitation energy transfer (EET) in chromophores-chlorop... more We present a quantum-mechanical study of excitation energy transfer (EET) in chromophores-chlorophylls, carotenoids and bilins-taken from structural models of photosynthetic proteins. The effects of the protein environment is analyzed in terms of variations of each single chromophore's properties and the screening of the chromophore-chromophore interaction. In particular, a distant and shape dependent screening effect is found in contrast to what generally assumed in previous models for EET.
ABSTRACT We investigate how electronic energy transfer in a series of three ethyne- linked zinc- ... more ABSTRACT We investigate how electronic energy transfer in a series of three ethyne- linked zinc- and free base tetraarylporphyrin dimers is tuned by the type of linker and by substitution on the porphyrin rings. We use time-dependent density functional theory (TD-DFT) combined with a recently developed fully polarizable QM/MM/PCM method. This allows us to dissect the bridge-mediated contributions to energy transfer in terms of superexchange (through-bond) interactions and Coulomb (through-space) terms mediated by the polarizability of the bridge. We explore the effects of the substituents and of the bridge-chromophore mutual orientation on these contributions. We find that bridge-mediated superexchange contributions largely boost energy transfer between the porphyrin units. When the effect of the solvent is also considered through the polarizable continuum model (PCM), we find good agreement with the through-bond versus through-space contributions determined experimentally, thus indicating the need to properly include both solvent and bridge effects in the study of energy transfer in bridged molecular dyads.
ABSTRACT The possibility to optimize optoelectronic devices, such as organic light-emitting diode... more ABSTRACT The possibility to optimize optoelectronic devices, such as organic light-emitting diodes or solar cells, by exploiting the special characteristics of triplet electronic states and their migration ability is attracting increased attention. In this study, we analyze how an intervening solvent modifies the distance dependence of triplet electronic energy transfer (TEET) processes by combining molecular dynamics simulations with quantum chemical calculations of the transfer matrix elements using the Fragment Excitation Difference (FED) method. We determine the β parameter characterizing the exponential distance decay of TEET rates in a stacked perylene dimer in water, chloroform, and benzene solutions. Our results indicate that the solvent dependence of β (βvacuum = 5.14 Å–1 > βwater = 3.77 Å–1 > βchloroform = 3.61 Å–1 > βbenzene = 3.44 Å–1) can be rationalized adopting the McConnell model of superexchange, where smaller triplet energy differences between the donor and the solvent lead to smaller β constants. We also estimate the decay of hole transfer (HT) and excess electron transfer (EET) processes in the system using the Fragment Charge Difference (FCD) method and find that βTEET can be reasonably well approximated by the sum of βEET and βHT constants.
The use of the Förster model to predict the dynamics of resonant electronic energy transfer (RET)... more The use of the Förster model to predict the dynamics of resonant electronic energy transfer (RET) in a model donor-acceptor dyad (a terphenyl-bridged perylene diimide (PDI)-terrylene diimide (TDI) dyad molecule) embedded at low temperature in a PMMA matrix is tested against experiment. The relevant ingredients involved in the Förster rate for RET, namely electronic coupling, spectral overlap, and screening effects, are accounted for in a quantitative manner. Electronic couplings are obtained from time-dependent density functional theory calculations, and the effect of the PMMA environment is included both on the transition densities and on their interaction through the IEFPCM model. We find that the presence of the terphenyl bridge induces a slight delocalization of the PDI and TDI transition densities over the bridge originating in a 56% increase in the coupling and in the breakdown of the dipole-dipole approximation. The spectral overlap is determined on the basis of a detailed simulation of the homogeneously broadened donor emission and acceptor absorption line shapes determined by fitting the single molecule spectra measured at 1.2 K. The corresponding distribution of spectral overlap throughout the ensemble is then estimated by assuming an uncorrelated inhomogeneous line broadening for the donor and acceptor. Combining the calculated electronic couplings and spectral overlaps sampled from Monte Carlo realizations of the energetic disorder, we obtain a mean RET time (approximately 8 ps) and a distribution in reasonable agreement with experiment.
In this study, we revisit the protocol previously proposed within the framework of the Miertus-Sc... more In this study, we revisit the protocol previously proposed within the framework of the Miertus-Scrocco-Tomasi (MST) continuum model to define the cavity between the solute and solvent for predicting hydration free energies of univalent ions. The protocol relies on the use of a reduced cavity (around 10-15% smaller than the cavity used for neutral compounds) around the atom(s) bearing the formal charge. The suitability of this approach is examined here for a series of 47 univalent ions for which accurate experimental hydration free energies are available. Attention is also paid to the effect of the charge renormalization protocol used to correct uncertainties arising from the electron density located outside the solute cavity. The method presented here provides, with a minimum number of fitted parameters, reasonable estimates within the experimental error of the hydration free energy of ions (average relative error of 4.7%) and is able to reproduce solvation in water of both small and large ions.
Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study... more Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study of resonance energy transfer (RET). However, most of these calculations rely on approximate QM methods due to the computational limitations imposed by the size of typical donor-acceptor systems. In this work, we present a novel implementation that allows computing electronic couplings at the coupled cluster singles and doubles (CCSD) level of theory. Solvent effects are also taken into account through the polarizable continuum model (PCM). As a test case, we use a dimer of indole, a common model system for tryptophan, which is routinely used as an intrinsic fluorophore in Förster resonance energy transfer studies. We consider two bright π → π* states, one of which has charge transfer character. Lastly, the results are compared with those obtained by applying TD-DFT in combination with one of the most popular density functionals, B3LYP.
The nature of the coupling of the photoexcited chromophore with the environment in a prototypical... more The nature of the coupling of the photoexcited chromophore with the environment in a prototypical system like green fluorescent protein (GFP) is to date not understood, and its description still defies state-of-the-art multiscale approaches. To identify which theoretical framework of the chromophore-protein complex can realistically capture its essence, we employ here a variety of electronic-structure methods, namely, time-dependent density functional theory (TD-DFT), multireference perturbation theory (NEVPT2 and CASPT2), and quantum Monte Carlo (QMC) in combination with static point charges (QM/MM), DFT embedding (QM/DFT), and classical polarizable embedding through induced dipoles (QM/MMpol). Since structural modifications can significantly affect the photophysics of GFP, we also account for thermal fluctuations through extensive molecular dynamics simulations. We find that a treatment of the protein through static point charges leads to significantly blue-shifted excitation energies and that including thermal fluctuations does not cure the coarseness of the MM description. While TDDFT calculations on large cluster models indicate the need of a responsive protein, this response is not simply electrostatic: An improved description of the protein in the ground state or in response to the excitation of the chromophore via ground-state or state-specific DFT and MMpol embedding does not significantly modify the results obtained with static point charges. Through the use of QM/MMpol in a linear response formulation, a different picture in fact emerges in which the main environment response to the chromophore excitation is the one coupling the transition density and the corresponding induced dipoles. Such interaction leads to significant red-shifts and a satisfactory agreement with full QM cluster calculations at the same level of theory. Our findings demonstrate that, ultimately, faithfully capturing the effects of the environment in GFP requires a quantum treatment of large photoexcited regions but that a QM/classical model can be a useful approximation when extended beyond the electrostatic-only formulation.
In the last decade, much progress has been made in the understanding of DNA excited-state dynamic... more In the last decade, much progress has been made in the understanding of DNA excited-state dynamics. In this context, theoretical studies focused both on the photophysical properties of individual nucleobases as well as on the relevant interactions in assemblies of two or more bases have been a valuable tool for exploring decay mechanisms of excited states in DNA. In contrast to singlet excited states, our knowledge on the energetics and dynamics of triplet excited states is still largely limited to the properties of individual bases. Thus, despite the fact that triplet-triplet electronic energy transfer (TET) can initiate phototoxic reactions in DNA, such as the formation of thymine cyclobutane dimers, little is known about the strength of the electronic interactions and the timescales for TET in nucleobase p stacks: the factors that determine the fate of triplet states in native DNA. Therefore, the assignment of decay components measured through ultrafast spectroscopy experiments remains a difficult task owing to the fundamental uncertainty regarding the degree of delocalization of triplet excited states and the approximate timescales for their migration. Herein, we present a study of TET between stacked adenine-adenine (A-A) and tymine-thymine (T-T) in polyA-polyT DNA sequences. We applied the semiempirical ZINDO method to investigate how DNA structural dynamics modulate the couplings for TET along a 15 ns classical molecular-dynamics (MD) trajectory. The suitability of the ZINDO method for describing the energetics and TET couplings of low-lying p!p* triplet states was validated by comparison with equation-of-motion coupled-cluster models with single and double substitutions (EOM-CCSD) and
This contribution presents a detalied theoretical study on how proteins regulate the electronic c... more This contribution presents a detalied theoretical study on how proteins regulate the electronic couplings responsible for exciton delocalization and electronic energy transfer (EET) in photosynthetic pigmentprotein complexes. Understanding environment effects, which cause line broadening and screen electronic interactions, is fundamentally important because of its central role in the control of EET dynamics. Recent work has furthermore shown that simple models for solvation may not be sufficient to explain effects that go beyond Förster theory, such as coherent contribution to energy transfer. Here, we focus on the phycobiliprotein PE545 from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24,3 and apply a novel combined quantum mechanics/molecular mechanics (QM/MM) method4 that explicitly incorporates environment polarization (protein and solvent) at the atomic level on the calculation of site energies and electronic couplings, thus going beyond the continuum dielectr...
We present the formulation and implementation of a polarizable quantum mechanics/molecular mechan... more We present the formulation and implementation of a polarizable quantum mechanics/molecular mechanics (QM/MM) strategy to describe environment effects in multiconfiguration self-consistent field calculations. The strategy is applied to the calculation of the vertical absorption spectrum of cytosine in water. In our approach, mutual polarization of the solute and the solvent is solved self-consistently at the complete-active-space self-consistent-field (CASSCF) level, and the resulting set of charges and dipoles is used to calculate vertical excitation energies using the complete-active-space second-order perturbative (CASPT2) approach and its multistate (MS-CASPT2) variant. In order to treat multiple excited states, we converge the solvent polarization with respect to the state-averaged density of the solute. In order to obtain the final energies, however, we introduce a state-specific correction, where the solvent polarization is recomputed with the density of each state, and demonstrate that this correction brings the excitation energies closer to the values obtained with state-optimized orbitals. Comparison with PCM and nonpolarizable QM/MM calculations shows the importance of specific solute-solvent interactions and environment polarization in describing experiments. Overall, the calculated excitations for the π → π* states in water show good agreement with the experimental spectrum, whereas the n → π* appear at energies above 6 eV, approximately 1 eV higher than in the gas phase. Beyond solvents, the new method will allow studying the impact of heterogeneous biological environments in multiple excited states, as well as the treatment of multichromophoric systems where charge transfer and exciton states play important roles.
Electronic energy transfer is reviewed with a particular emphasis on its role in photosynthesis. ... more Electronic energy transfer is reviewed with a particular emphasis on its role in photosynthesis. The article describes the advances in theory that have been motivated by studies of photosynthetic light harvesting antenna proteins. Noting that most theoretical work presently focuses on just a few photosynthetic systems, the extraordinary scope and diversity of systems actually found in nature is described.
Advances in electronic spectroscopies with femtosecond time resolution have provided new informat... more Advances in electronic spectroscopies with femtosecond time resolution have provided new information on the excitonic processes taking place during the energy conversion in natural photosynthetic antennae. This has promoted the development of new theoretical protocols aiming at accurately describing the properties and mechanisms of exciton formation and relaxation. In this perspective, we provide an overview of the quantum chemical based approaches, trying to underline both the potentials of the methods and their weaknesses. In particular three main aspects will be analysed, the quantum mechanical description of excitonic parameters (site energies and couplings), the incorporation of environmental effects on these parameters through hybrid quantum/classical approaches, and the modelling of the dynamical coupling among such parameters and the vibrations of the pigment-protein complex.
An extension of the Miertus-Scrocco-Tomasi (MST) continuum method to the Integral Equation Formal... more An extension of the Miertus-Scrocco-Tomasi (MST) continuum method to the Integral Equation Formalism (IEF) is presented. In particular, we report here the parametrization of the MST(IEF) model to the solvation in water, octanol, chloroform and carbon tetrachloride. A detailed comparison is made between the results obtained from the MST(PCM) formalism corrected by using diverse charge normalization schemes and those obtained from the IEF formalism. The IEF method is found to provide results in close agreement with those obtained within the PCM framework by taking into account the anisotropy of the solute's charge distribution in the charge normalization of the apparent surface charge that simulates the solvent reaction field. Besides the standard HF/6-31G(d) level of theory considered in previous parametrizations of the MST(PCM) model, we also report here the results obtained for the B3LYP hybrid density functional method. These results indicate that there are small differences in the electrostatic component of the solvation free energy determined from HF and B3LYP levels of theory, which might be captured by suitable adjustment of the atomic surface tensions in the van der Waals component. Overall, the results support the strategy used in the development of the MST model and its suitability as a robust approach to the study of molecules in solution. q
ABSTRACT A combined molecular dynamics and a polarizable quantum mechanics (QM)/molecular mechani... more ABSTRACT A combined molecular dynamics and a polarizable quantum mechanics (QM)/molecular mechanics (MM) approach can be used to obtain a reliable picture of the excitonic properties of the Fenna–Matthews–Olson (FMO) protein, as shown on p. 3194, by B. Mennucci et al.
Excitation energy transfer involving semiconductor quantum dots (QDs) has received increased atte... more Excitation energy transfer involving semiconductor quantum dots (QDs) has received increased attention in recent years because their properties, such as high photostability and size-tunable optical properties, have made QDs attractive as F rster resonant energy transfer (FRET) ...
Long-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low... more Long-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low and at room temperatures have generated a heated debate over the impact that the coupling of electronic excitations to molecular vibrations of the relevant actors (pigments, proteins and solvents) has on the excitation energy transfer process. In this work, we use a combined MD and QM/MMPol strategy to investigate the exciton-phonon interactions in the PE545 light-harvesting complex by computing the spectral densities for each pigment and analyzing their consequences in the exciton dynamics. Insights into the origin of relevant peaks, as well as their differences among individual pigments, are provided by correlating them with normal modes obtained from a quasi-harmonic analysis of the motions sampled by the pigments in the complex. Our results indicate that both the protein and the solvent significantly modulate the intramolecular vibrations of the pigments thus playing an important role in promoting or suppressing certain exciton-phonon interactions. We also find that these low-frequency features are largely smoothed out when the spectral density is averaged over the complex, something difficult to avoid in experiments that underscores the need to combine theory and experiment to understand the origin of quantum coherence in photosynthetic light-harvesting.
International Conference on Ultrafast Phenomena, 2010
Page 1. Quantum-Coherent Energy Transfer in Marine Algae at Ambient Temperature via Ultrafast Pho... more Page 1. Quantum-Coherent Energy Transfer in Marine Algae at Ambient Temperature via Ultrafast Photon Echo Studies Cathy Y. Wong, Hoda Hossein-Nejad, Carles Curutchet and Gregory D. Scholes* Department of Chemistry, 80 St. ...
We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analy... more We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.
We present a quantum-mechanical study of excitation energy transfer (EET) in chromophores-chlorop... more We present a quantum-mechanical study of excitation energy transfer (EET) in chromophores-chlorophylls, carotenoids and bilins-taken from structural models of photosynthetic proteins. The effects of the protein environment is analyzed in terms of variations of each single chromophore's properties and the screening of the chromophore-chromophore interaction. In particular, a distant and shape dependent screening effect is found in contrast to what generally assumed in previous models for EET.
ABSTRACT We investigate how electronic energy transfer in a series of three ethyne- linked zinc- ... more ABSTRACT We investigate how electronic energy transfer in a series of three ethyne- linked zinc- and free base tetraarylporphyrin dimers is tuned by the type of linker and by substitution on the porphyrin rings. We use time-dependent density functional theory (TD-DFT) combined with a recently developed fully polarizable QM/MM/PCM method. This allows us to dissect the bridge-mediated contributions to energy transfer in terms of superexchange (through-bond) interactions and Coulomb (through-space) terms mediated by the polarizability of the bridge. We explore the effects of the substituents and of the bridge-chromophore mutual orientation on these contributions. We find that bridge-mediated superexchange contributions largely boost energy transfer between the porphyrin units. When the effect of the solvent is also considered through the polarizable continuum model (PCM), we find good agreement with the through-bond versus through-space contributions determined experimentally, thus indicating the need to properly include both solvent and bridge effects in the study of energy transfer in bridged molecular dyads.
ABSTRACT The possibility to optimize optoelectronic devices, such as organic light-emitting diode... more ABSTRACT The possibility to optimize optoelectronic devices, such as organic light-emitting diodes or solar cells, by exploiting the special characteristics of triplet electronic states and their migration ability is attracting increased attention. In this study, we analyze how an intervening solvent modifies the distance dependence of triplet electronic energy transfer (TEET) processes by combining molecular dynamics simulations with quantum chemical calculations of the transfer matrix elements using the Fragment Excitation Difference (FED) method. We determine the β parameter characterizing the exponential distance decay of TEET rates in a stacked perylene dimer in water, chloroform, and benzene solutions. Our results indicate that the solvent dependence of β (βvacuum = 5.14 Å–1 > βwater = 3.77 Å–1 > βchloroform = 3.61 Å–1 > βbenzene = 3.44 Å–1) can be rationalized adopting the McConnell model of superexchange, where smaller triplet energy differences between the donor and the solvent lead to smaller β constants. We also estimate the decay of hole transfer (HT) and excess electron transfer (EET) processes in the system using the Fragment Charge Difference (FCD) method and find that βTEET can be reasonably well approximated by the sum of βEET and βHT constants.
The use of the Förster model to predict the dynamics of resonant electronic energy transfer (RET)... more The use of the Förster model to predict the dynamics of resonant electronic energy transfer (RET) in a model donor-acceptor dyad (a terphenyl-bridged perylene diimide (PDI)-terrylene diimide (TDI) dyad molecule) embedded at low temperature in a PMMA matrix is tested against experiment. The relevant ingredients involved in the Förster rate for RET, namely electronic coupling, spectral overlap, and screening effects, are accounted for in a quantitative manner. Electronic couplings are obtained from time-dependent density functional theory calculations, and the effect of the PMMA environment is included both on the transition densities and on their interaction through the IEFPCM model. We find that the presence of the terphenyl bridge induces a slight delocalization of the PDI and TDI transition densities over the bridge originating in a 56% increase in the coupling and in the breakdown of the dipole-dipole approximation. The spectral overlap is determined on the basis of a detailed simulation of the homogeneously broadened donor emission and acceptor absorption line shapes determined by fitting the single molecule spectra measured at 1.2 K. The corresponding distribution of spectral overlap throughout the ensemble is then estimated by assuming an uncorrelated inhomogeneous line broadening for the donor and acceptor. Combining the calculated electronic couplings and spectral overlaps sampled from Monte Carlo realizations of the energetic disorder, we obtain a mean RET time (approximately 8 ps) and a distribution in reasonable agreement with experiment.
In this study, we revisit the protocol previously proposed within the framework of the Miertus-Sc... more In this study, we revisit the protocol previously proposed within the framework of the Miertus-Scrocco-Tomasi (MST) continuum model to define the cavity between the solute and solvent for predicting hydration free energies of univalent ions. The protocol relies on the use of a reduced cavity (around 10-15% smaller than the cavity used for neutral compounds) around the atom(s) bearing the formal charge. The suitability of this approach is examined here for a series of 47 univalent ions for which accurate experimental hydration free energies are available. Attention is also paid to the effect of the charge renormalization protocol used to correct uncertainties arising from the electron density located outside the solute cavity. The method presented here provides, with a minimum number of fitted parameters, reasonable estimates within the experimental error of the hydration free energy of ions (average relative error of 4.7%) and is able to reproduce solvation in water of both small and large ions.
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Papers by Carles Curutchet