Lorenzo Cupellini

A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes

Nonlinear electronic spectroscopies represent one of the most powerful techniques to study complex multichromophoric architectures. For these systems, in fact, linear spectra are too congested to be used to disentangle the many coupled vibroelectronic processes that are activated. By using a 2D approach, instead, a clear picture can be achieved, but only when the recorded spectra are combined with a proper interpretative model. So far, this has been almost always achieved through parametrized exciton Hamiltonians that necessarily introduce biases and/or arbitrary assumptions. In this study, a first-principles approach is presented that combines accurate quantum chemical descriptions with state-of-the-art models for the environment through the use of atomistic and polarizable embeddings. Slow and fast bath dynamics, along with exciton transport between the pigments, are included. This approach is applied to the 2DES spectroscopy of the Light-Harvesting 2 (LH2) complex of purple bacteria. Simulations are extended over the entire visible-near-infrared spectral region to cover both carotenoid and bacteriochlorophyll signals. Our results provide an accurate description of excitonic properties and relaxation pathways, and give an unprecedented insight into the interpretation of the spectral signatures of the measured 2D signals.

Electronic Excitations in Nonpolar Solvents: Can the Polarizable Continuum Model Accurately Reproduce Solvent Effects?

In nonpolar solvents, both electrostatic and nonelectrostatic interactions play a role in tuning the electronic excitations of molecular solutes. This specificity makes the application of continuum solvation models a challenge. Here, we propose a strategy for the calculation of solvatochromic shifts on absorption spectra, using a coupling of the polarizable continuum model with a time-dependent density functional theory framework, which explicitly accounts for dispersion and repulsion, as well as for electrostatic effects. Our analysis makes a step further in the interpretation of the effects of nonpolar solvents and suggests new directions in their modeling using continuum formulations.

Plasmon enhanced light harvesting: multiscale modeling of the FMO protein coupled with gold nanoparticles.

Plasmonic systems, such as metal nanoparticles, are becoming increasingly important in spectroscopies and devices because of their ability to enhance, even by several orders of magnitude, the photophysical properties of neighboring systems. In particular, it has been shown both theoretically and experimentally that combining nanoplasmonic devices with natural light-harvesting proteins substantially increases the fluorescence and absorption properties of the system. This kind of biohybrid device can have important applications in the characterization and design of efficient light-harvesting systems. In the present work, the FMO light-harvesting protein was combined with gold nanoparticles of different sizes, and its photophysical properties were characterized using a multiscale quantum-mechanical classical-polarizable and continuum model (QM/MMPol/PCM). By optimal tuning of the plasmon resonance of the metal nanoparticles, fluorescence enhancements of up to 2 orders of magnitude were observed. Orientation effects were found to be crucial: amplifications by factors of up to 300 were observed for the absorption process, while the radiative decay of the emitting state increased at most by a factor of 10, mostly as a result of poor alignment of the emitting state with the considered metal aggregates. Despite being a limiting factor for high-fluorescence-enhancement devices, the strong orientation dependence may represent an important feature of the natural light-harvesting system that could allow selective enhancement of a specific excited state of the complex.

EXAT: EXcitonic analysis tool

We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single‐chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV‐vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on‐screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G‐quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/.

The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria

The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular–level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800–850 and B800–820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift.

Density-Dependent Formulation of Dispersion–Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

Mixed QM/MM models are widely used to explore the structure, reactivity and electronic properties of complex chemical systems. Whereas such models typically include electrostatics, and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, non-electrostatic dispersion and repulsion interactions are instead commonly described through classical potentialsMixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdWTS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdWTS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Coherence in carotenoid-to-chlorophyll energy transfer

The subtle details of the mechanism of energy flow from carotenoids to chlorophylls in biological light-harvesting complexes are still not fully understood, especially in the ultrafast regime. Here we focus on the antenna complex peridinin–chlorophyll a–protein (PCP), known for its remarkable efficiency of excitation energy transfer from carotenoids—peridinins—to chlorophylls. PCP solutions are studied by means of 2D electronic spectroscopy in different experimental conditions. Together with a global kinetic analysis and multiscale quantum chemical calculations, these data allow us to comprehensively address the contribution of the potential pathways of energy flow in PCP. These data support dominant energy transfer from peridinin S2 to chlorophyll Qy state via an ultrafast coherent mechanism. The coherent superposition of the two states is functional to drive population to the final acceptor state, adding an important piece of information in the quest for connections between coherent phenomena and biological functions.Energy transfer from carotenoids to chlorophylls in light-harvesting is still not fully understood, especially in the ultrafast regime. Here, the authors investigate the coherent dynamics of this process in peridinin-chlorophyll a-protein complex via 2D electronic spectroscopy and quantum chemical calculations.

Atomic Detail of Protein Folding Revealed by an Ab Initio Reappraisal of Circular Dichroism

Circular dichroism (CD) is known to be an excellent tool for the determination of protein secondary structure due to fingerprint signatures of α and β domains. However, CD spectra are also sensitive to the 3D arrangement of the chain as a result of the excitonic nature of additional signals due to the aromatic residues. This double sensitivity, when extended to time-resolved experiments, should allow protein folding to be monitored with high spatial resolution. To date, the exploitation of this very appealing idea has been limited, due to the difficulty in relating the observed spectral evolution to specific configurations of the chain. Here, we demonstrate that the combination of atomistic molecular dynamics simulations of the folding pathways with a quantum chemical evaluation of the excitonic spectra provides the missing key. This is exemplified for the folding of canine milk lysozyme protein.

Frenkel-exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems: FEDA of CD and CPL for Multichromophoric Systems

Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through‐space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge‐invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible.

Electronic energy transfer in biomacromolecules

Electronic energy transfer is widely used as a molecular ruler to interrogate the structure of biomacromolecules, and performs a key task in photosynthesis by transferring collected energy through specialized pigment–protein complexes. Förster theory, introduced over 70 years ago, allows linking transfer rates to simple structural and spectroscopic properties of the energy‐transferring molecules. In biosystems, however, significant deviations from Förster behavior often arise due to breakdown of the ideal dipole approximation, dielectric screening effects due to the biological environment, or departure from the weak‐coupling regime. In this review, we provide a concise overview of advances in simulations of energy transfer in biomacromolecules that allow overcoming the main limitations of Förster theory. We first discuss advances in quantum chemical methods to compute electronic couplings, their extension to multiscale formulations to include screening effects, and strategies to treat the interplay between coupling fluctuations and energy transfer dynamics. We then examine the spectral overlap term, and how this quantity can be estimated from simulations of the spectral density of exciton–phonon coupling. Finally, we discuss rate theories that can describe energy transfers in situations where strong coupling leads to delocalized excitions, a common situation found in closely packed multichromophoric systems such as photosynthetic complexes and nucleic acids.