Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. Here, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-adiabatic excited-state molecular dynamics simulations, we show that the non-radiative relaxation is accelerated with the number of stacked molecules. This effect is explained by differences in the energy splitting between states that impacts their corresponding nonadiabatic couplings. Additionally, our analysis of the vibronic dynamics reveals that the passage through the different conical intersections that participate in the relaxation of the stacked systems, activate a positive feedback mechanism. This effect involves a narrow set of vibrational normal modes that accelerate the process by increasing the efficiency of its vibronic dynamics. In contrast, an addition of a biologically inspired backbone slows down the relaxation rate due to its participation in the vibronic dynamics of the molecular stacking arrangements. Our results suggest the stacking arrangements and common backbones as strategies to modulate the efficiency of electronic and vibrational relaxation of diimide-based systems and other molecular aggregates.
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Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates
A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards a study of the highly flexible water-solvated adenine–adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display various intermolecular arrangements, known to deeply affect their photochemical outcome. Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the complexity of the flexible ApA conformational space. By using our sum-over-states (SOS) approach to obtain the 2DES spectra for each of these selected conformations, we can discern spectral changes and relate them to specific nuclear arrangements: close lying π-stacked bases exhibit a splitting of their respective 1 L a signal traces; T-stacked bases exhibit the appearance of charge transfer states in the low-energy Vis probing window while displaying no 1 L a splitting, being particularly favoured when promoting amino to 5-ring interactions; unstacked and distant adenine moieties exhibit signals similar to those of the adenine monomer, as is expected for non-interacting nucleobases. 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. This is expected to aid the understanding of how nucleobase aggregation controls and modulates the photostability and photo-damage of extended DNA/RNA systems.
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- Award ID(s):
- 1663822
- NSF-PAR ID:
- 10057302
- Date Published:
- Journal Name:
- Faraday Discussions
- Volume:
- 207
- ISSN:
- 1359-6640
- Page Range / eLocation ID:
- 233 to 250
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Electron transfer (ET) in donor–bridge–acceptor (DBA) compounds depends strongly on the structural and electronic properties of the bridge. Among the bridges that support donor–acceptor conjugation, alkyne bridges have attractive and unique properties: they are compact, possess linear structure permitting access to high symmetry DBA molecules, and allow torsional motion of D and A, especially for longer bridges. We report conformation dependent electron transfer dynamics in a set of novel DBA compounds featuring butadiyne (C4) bridge, N -isopropyl-1,8-napthalimide (NAP) acceptors, and donors that span a range of reduction potentials (trimethyl silane (Si-C4-NAP), phenyl (Ph-C4-NAP), and dimethyl aniline (D-C4-NAP)). Transient mid-IR absorption spectra of the CC bridge stretching modes, transient spectra in the visible range, and TD-DFT calculations were used to decipher the ET mechanisms. We found that the electronic excited state energies and, especially, the transition dipoles (S 0 → S n ) depend strongly on the dihedral angle ( θ ) between D and A and the frontier orbital symmetry, offering an opportunity to photo-select particular excited states with specific ranges of dihedral angles by exciting at chosen wavelengths. For example, excitation of D-C4-NAP at 400 nm predominantly prepares an S 1 excited state in the planar conformations ( θ ∼ 0) but selects an S 2 state with θ ∼ 90°, indicating the dominant role of the molecular symmetry in the photophysics. Moreover, the symmetry of the frontier orbitals of such DBA compounds not only defines the photo-selection outcome, but also determines the rate of the S 2 → S 1 charge separation reaction. Unprecedented variation of the S 2 –S 1 electronic coupling with θ by over four orders of magnitude results in slow ET at θ ca. 0° and 90° but extremely fast ET at θ of 20–60°. The unique features of high-symmetry alkyne bridged DBA structures enable frequency dependent ET rate selection and make this family of compounds promising targets for the vibrational excitation control of ET kinetics.more » « less
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na (Ed.)NMR chemical shifts provide a sensitive probe of protein structure and dynamics. Prediction of shifts, and therefore interpretation of shifts, particularly for the frequently measured amidic 15N sites, remains a tall challenge. We demonstrate that protein 15N chemical shift prediction from QM/MM predictions can be improved if conformational variation is included via MD sampling, focusing on the antibiotic target, E. coli Dihydrofolate reductase (DHFR). Variations of up to 25 ppm in predicted 15N chemical shifts are observed over the trajectory. For solution shifts the average of fluctuations on the low picosecond timescale results in a superior prediction to a single optimal conformation. For low temperature solid state measurements, the histogram of predicted shifts for locally minimized snapshots with specific solvent arrangements sampled from the trajectory explains the heterogeneous linewidths; in other words, the conformations and associated solvent are ‘frozen out’ at low temperatures and result in inhomogeneously broadened NMR peaks. We identified conformational degrees of freedom that contribute to chemical shift variation. Backbone torsion angles show high amplitude fluctuations during the trajectory on the low picosecond timescale. For a number of residues, including I60, ψ varies by up to 60º within a conformational basin during the MD simulations, despite the fact that I60 (and other sites studied) are in a secondary structure element and remain well folded during the trajectory. Fluctuations in ψ appear to be compensated by other degrees of freedom in the protein, including φ of the succeeding residue, resulting in “rocking” of the amide plane with changes in hydrogen bonding interactions. Good agreement for both room temperature and low temperature NMR spectra provides strong support for the specific approach to conformational averaging of computed chemical shifts.more » « less
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Abstract Mesoscopic quantum systems exhibit complex many-body quantum phenomena, where interactions between spins and charges give rise to collective modes and topological states. Even simple, non-interacting theories display a rich landscape of energy states—distinct many-particle configurations connected by spin- and energy-dependent transition rates. The ways in which these energy states interact is difficult to characterize or predict, especially in regimes of frustration where many-body effects create a multiply degenerate landscape. Here, we use network science to characterize the complex interconnection patterns of these energy-state transitions. Using an experimentally verified computational model of electronic transport through quantum antidots, we construct networks where nodes represent accessible energy states and edges represent allowed transitions. We find that these networks exhibit Rentian scaling, which is characteristic of efficient transportation systems in computer circuitry, neural circuitry, and human mobility, and can be used to measure the interconnection complexity of a network. We find that the topological complexity of the state transition networks—as measured by Rent’s exponent— correlates with the amount of current flowing through the antidot system. Furthermore, networks corresponding to points of frustration (due, for example, to spin-blockade effects) exhibit an enhanced topological complexity relative to non-frustrated networks. Our results demonstrate that network characterizations of the abstract topological structure of energy landscapes capture salient properties of quantum transport. More broadly, our approach motivates future efforts to use network science to understand the dynamics and control of complex quantum systems.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/c7fd00201g
