Exciton-Exciton Annihilation Is Coherently Suppressed in H-Aggregates, but Not in J-Aggregates

We theoretically demonstrate a strong dependence of the annihilation rate between (singlet) excitons on the sign of dipole-dipole couplings between molecules. For molecular H-aggregates, where this sign is positive, the phase relation of the delocalized two-exciton wavefunctions causes a destructive interference in the annihilation probability. For J-aggregates, where this sign is negative, the interference is constructive instead, as a result of which no such coherent suppression of the annihilation rate occurs. As a consequence, room temperature annihilation rates of typical H- and J-aggregates differ by a factor of ~3, while an order of magnitude difference is found for low-temperature aggregates with a low degree of disorder. These findings, which explain experimental observations, reveal a fundamental principle underlying exciton-exciton annihilation, with major implications for technological devices and experimental studies involving high excitation densities

Zoochorous dispersal of freshwater bivalves: an overlooked vector in biological invasions?

Vectors that underpin the natural dispersal of invasive alien species are frequently unknown. In particular, the passive dispersal (zoochory) of one organism (or propagule) by another, usually more mobile animal, remains poorly understood. Field observations of the adherence of invasive freshwater bivalves to other organisms have prompted us to assess the importance of zoochory in the spread of three prolific invaders: zebra mussel Dreissena polymorpha; quagga mussel Dreissena bugensis; and Asian clam Corbicula fluminea. An extensive, systematic search of the literature was conducted across multiple on-line scientific databases using various search terms and associated synonyms. In total, only five publications fully satisfied the search criteria. It appears that some fish species can internally transport viable adult D. polymorpha and C. fluminea specimens. Additionally, literature indicates that veligers and juvenile D. polymorpha can adhere to the external surfaces of waterbirds. Overall, literature suggests that zoochorous dispersal of invasive bivalves is possible, but likely a rare occurrence. However, even the establishment of a few individuals (or a single self-fertilising C. fluminea specimen) can, over-time, result in a substantial population. Here, we highlight knowledge gaps, identify realistic opportunities for data collection, and suggest management protocols to mitigate the spread of invasive alien species

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D2O and compare with experimental observations.Netherlands Organization for Scientific Research (VIDI grant)National Science Foundation (U.S.) ((NSF) CHE-0911107

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

Quantum-Classical Simulation of Molecular Motors Driven Only by Light

[Image: see text] Molecular motors that exhibit controlled unidirectional rotation provide great prospects for many types of applications, including nanorobotics. Existing rotational motors have two key components: photoisomerization around a π-bond followed by a thermally activated helical inversion, the latter being the rate-determining step. We propose an alternative molecular system in which the rotation is caused by the electric coupling of chromophores. This is used to engineer the excited state energy surface and achieve unidirectional rotation using light as the only input and avoid the slow thermally activated step, potentially leading to much faster operational speeds. To test the working principle, we employ quantum-classical calculations to study the dynamics of such a system. We estimate that motors built on this principle should be able to work on a subnanosecond time scale for such a full rotation. We explore the parameter space of our model to guide the design of a molecule that can act as such a motor

Modeling the Effect of Disorder in the Two-Dimensional Electronic Spectroscopy of Poly-3-hexyltiophene in an Organic Photovoltaic Blend:A Combined Quantum/Classical Approach

We introduce a first-principles model of the 12-mer poly-3-hexyltiophene (P3HT) polymer system in the realistic description of an organic photovoltaic blend environment. We combine Molecular Dynamics (MD) simulations of a thin-film blend of P3HT and phenyl-C61-butyric acid methyl ester (PCBM) to model the interactions with a fluctuating environment with Time-Dependent Density Functional Theory (TDDFT) calculations to parametrize the effect of the torsional flexibility in the polymer and construct an exciton-type Hamiltonian that describes the photoexcitation of the polymer. This allows us to reveal the presence of different flexibility patterns governed by the torsional angles along the polymer chain which, in the interacting fluctuating environment, control the broadening of the spectral observables. We identify the origin of the homogeneous and inhomogeneous line shape of the simulated optical signals. This is paramount to decipher the spectroscopic nature of the ultrafast electron-transfer process occurring in organic photovoltaic (OPV) materials

AIM:A Mapping Program for Infrared Spectroscopy of Proteins

[Image: see text] Here, we present a new analysis program, AIM, that allows extracting the vibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infrared spectroscopy modeling. The constructed Hamiltonians can be used as input for spectral calculations allowing the calculation of infrared absorption spectra, vibrational circular dichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of the structure and dynamics of proteins. We will explain the essence of how AIM works and give examples of the information and spectra that can be obtained with the program using the Trypsin Inhibitor as an example. AIM is freely available from GitHub, and the package contains a demonstration allowing easy introduction to the use of the program

Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy

Here, we performed spectral simulations of the amide-I vibrational spectra for three proposed fibril structures of the human islet amyloid polypeptide, which is involved in type II diabetes. We modeled both the overall absorption and two-dimensional infrared spectra for these structures. We further analyzed the isotope-labeled spectra, including the variation between structures. The analysis suggests that the infrared spectra of the cryo-electron microscopy structure provide the best match with experimental data. We further simulated isotope-labeled dilu- tion spectroscopy investigating the correlation between the predicted spectral peak shift and the coupling between the amide units. While this correlation works in most cases, failures were observed when the isotope-labeled spectra were broad compared to the coupling or exhibited structure. These findings will be useful in the quest for potential toxic fibril formation intermediates

Optical Signatures of the Coupling between Excitons and Charge Transfer States in Linear Molecular Aggregates

Charge Transfer (CT) has enjoyed continuous interest due to increasing experimental control over molecular structure leading to applications in, for example, photovoltaics and hydrogen production. In this paper, we investigate the effect of CT states on the absorption spectrum of linear molecular aggregates using a scattering matrix technique that allows us to deal with arbitrarily large systems. The presented theory performs well for both strong and weak mixing of exciton and CT states, bridging the gap between previously employed methods which are applicable in only one of these limits. In experimental spectra the homogeneous linewidth is often too large to resolve all optically allowed transitions individually, resulting in a characteristic two-peak absorption spectrum in both the weak- and strong-coupling regime. Using the scattering matrix technique we examine the contributions of free and bound states in detail. We conclude that the skewness of the high-frequency peak may be used as a new way to identify the exciton-CT-state coupling strength.Comment: 12 pages, 9 figure