Tuning Electronic Relaxation of Nanorings Through Their Interlocking.

Electronic and vibrational relaxation processes can be optimized and tuned by introducing alternative pathways that channel excess energy more efficiently. An ensemble of interacting molecular systems can help overcome the bottlenecks caused by large energy gaps between intermediate excited states involved in the relaxation process. By employing this strategy, catenanes composed of mechanically interlocked carbon nanostructures show great promise as new materials for achieving higher efficiencies in electronic devices.

Nonadiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation.

In this article, the nonadiabatic excited-state Molecular dynamics (NEXMD) package is linked with the SANDER package, provided by AMBERTOOLS. The combination of these software packages enables the simulation of photoinduced dynamics of large multichromophoric conjugated molecules involving several coupled electronic excited states embedded in an explicit solvent by using the quantum/mechanics/molecular mechanics (QM/MM) methodology. The fewest switches surface hopping algorithm, as implemented in NEXMD, is used to account for quantum transitions among the adiabatic excited-state simulations of the photoexcitation and subsequent nonadiabatic electronic transitions, and vibrational energy relaxation of a substituted polyphenylenevinylene oligomer (PPV3-NO2) in vacuum and methanol as an explicit solvent has been used as a test case.

Transient-absorption spectroscopy of dendrimers nonadiabatic excited-state dynamics simulations.

The efficiency of light-harvesting and energy transfer in multi-chromophore ensembles underpins natural photosynthesis. Dendrimers are highly branched synthetic multi-chromophoric conjugated supra-molecules that mimic these natural processes. After photoexcitation, their repeated units participate in a number of intramolecular electronic energy relaxation and redistribution pathways that ultimately funnel to a sink.

Electronic Couplings versus Thermal Fluctuations in the Internal Conversion of Perylene Diimides: The Battle to Localize the Exciton.

Energy transfer processes among units of light-harvesting homo-oligomers impact the efficiency of these materials as components in organic optoelectronic devices such as solar cells. Perylene diimide (PDI), a prototypical dye, features exceptional light absorption and highly tunable optical and electronic properties. These properties can be modulated by varying the number of PDI units and linkers between them.

Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers.

Charge-transfer (CT) excited states play an important role in many biological processes. However, many computational approaches often inadequately address the equilibration effects of nuclear and environmental degrees of freedom on these states. One prominent example of systems in which CT states are of utmost importance is reaction centers (RC) in photosystems.

Resolving the Puzzle of Charge Carrier Lifetime in ZnO by Revisiting the Role of Oxygen Vacancy.

Zinc oxide (ZnO) is a wide bandgap prototypical n-type semiconductor due to the presence of intrinsic oxygen vacancies (V). The V can readily transfer to the most energetically favorable +2 charged V (V) by losing two electrons mediated by the metastable V defect. Nevertheless, the influence of charged V on the charge dynamics in ZnO and the underlying mechanisms remain elusive.

Twisting Aromaticity and Photoinduced Dynamics in Hexapole Helicenes.

Curved aromatic molecules are attractive electronic materials, where an additional internal strain uniquely modifies their structure, aromaticity, dynamics, and optical properties. Helicenes are examples of such twisted conjugated systems. Herein, we analyze the photoinduced dynamics in different stereoisomers of a hexapole helicene by using nonadiabatic excited-state molecular dynamics simulations.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.

Vibrational Funnels for Energy Transfer in Organic Chromophores.

Photoinduced intramolecular energy transfers in multichromophoric molecules involve nonadiabatic vibronic channels that act as energy transfer funnels. They commonly take place through specific directions of motion dictated by the nonadiabatic coupling vectors. Vibrational funnels may support persistent coherences between electronic states and sometimes delineate the presence of minor alternative energy transfer pathways.

Impact of the core on the inter-branch exciton exchange in dendrimers.

Organic dendrimers with π conjugated systems are capable of capturing solar energy as a renewable source for human use. Nonetheless, further study regarding the relationship between the structure and the energy transfer mechanism in these types of molecules is still necessary. In this work, nonadiabatic excited state molecular dynamics (NEXMD) were carried out to study the intra- and inter-branch exciton migration in two tetra-branched dendrimers, C(dSSB) and Ad(BuSSB), which differ in their respective carbon and adamantane core.

Monitoring vibronic coherences and molecular aromaticity in photoexcited cyclooctatetraene with an X-ray probe: a simulation study.

Understanding conical intersection (CI) dynamics and subsequent conformational changes is key for exploring and controlling photo-reactions in aromatic molecules. Monitoring of their time-resolved dynamics remains a formidable experimental challenge. In this study, we simulate the photoinduced S to S non-adiabatic dynamics of cyclooctatetraene (COT), involving multiple CIs with relaxation times in good agreement with experiment.

Exciton-vibrational dynamics induces efficient self-trapping in a substituted nanoring.

Cycloparaphenylenes, being the smallest segments of carbon nanotubes, have emerged as prototypes of the simplest carbon nanohoops. Their unique structure-dynamics-optical properties relationships have motivated a wide variety of synthesis of new related nanohoop species. Studies of how chemical changes, introduced in these new materials, lead to systems with new structural, dynamics and optical properties, expand their functionalities for optoelectronics applications.

Charge-Transfer Luminescence in a Molecular Donor-Acceptor Complex: Computational Insights.

Donor-acceptor molecular complexes are a popular class of materials utilizing charge-transfer states for practical applications. A recent class of donor-acceptor dyads based on the fluorescent BODIPY functionalized with triphenylamine (TPA) shows the peculiar property of dual fluorescence. It is hypothesized that instead of the sensitized charge-transfer state being optically dark, it provides an additional bright radiative pathway.

Infinitene: Computational Insights from Nonadiabatic Excited State Dynamics.

Progress in organic synthesis opens exploration of a rich diversity of molecules with interesting new structural topologies. This is the case of a recently synthesized helically twisted figure-eight molecule coined infinitene. The molecule belongs to a numerous family of looped polyarenes, where the degree of π-conjugation is controlled by high strain energies and steric hindrances.

Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation.

We present a method to link the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) package to the SANDER package supplied by AMBERTOOLS to provide excited-state adiabatic quantum mechanics/molecular mechanics (QM/MM) simulations. NEXMD is a computational package particularly developed to perform simulations of the photoexcitation and subsequent nonadiabatic electronic and vibrational energy relaxation in large multichromophoric conjugated molecules involving several coupled electronic excited states. The NEXMD-SANDER exchange has been optimized in order to achieve excited-state adiabatic dynamics simulations of large conjugated materials in a QM/MM environment, such as an explicit solvent.

Ultrafast coherent photoexcited dynamics in a trimeric dendrimer probed by X-ray stimulated-Raman signals.

The photoinduced ultrafast coherent inter-chromophore energy redistribution in a triarylamine trimer is explored using nonadiabatic excited state molecular dynamics followed by simulations of X-ray Raman signals. The nitrogencentered system ensures strong interchromophore interactions and, thus, the presence of coherences. Nevertheless, the multitude of non-deterministic photoinduced pathways during the ultrafast inter-branch migration of the excitation results in random confinement on some branches and, therefore, spatial exciton scrambling and loss of phase information at long times.

Depleted Oxygen Defect State Enhancing Tungsten Trioxide Photocatalysis: A Quantum Dynamics Perspective.

Oxygen vacancies generally create midgap states in transition metal oxides, which are expected to decrease the photoelectrochemical water-splitting efficiency. Recent experiments defy this expectation but leave the mechanism unclear. Focusing on the photoanode WO as a prototypical system, we demonstrate using nonadiabatic molecular dynamics that an oxygen vacancy suppresses nonradiative electron-hole recombination, because the defect acts as an electron reservoir instead of a recombination center.

Impact of protein conformational diversity on AlphaFold predictions.

Motivation: After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins, for example, challenges the structural prediction methods because the models should represent a set of conformers instead of single structures. The evolutionary and structural features captured by effective deep learning techniques may unveil the information to generate several diverse conformations from a single sequence.

Vibronic Photoexcitation Dynamics of Perylene Diimide: Computational Insights.

Perylene diimide (PDI) represents a prototype material for organic optoelectronic devices because of its strong optical absorbance, chemical stability, efficient energy transfer, and optical and chemical tunability. Herein, we analyze in detail the vibronic relaxation of its photoexcitation using nonadiabatic excited-state molecular dynamics simulations. We find that after the absorption of a photon, which excites the electron to the second excited state, S, induced vibronic dynamics features persistent modulations in the spatial localization of electronic and vibrational excitations.

Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility.

Dynamics of protein cavities associated with protein fluctuations and conformational plasticity is essential for their biological function. NMR ensembles, molecular dynamics (MD) simulations, and normal mode analysis (NMA) provide appropriate frameworks to explore functionally relevant protein dynamics and cavity changes relationships. Within this context, we have recently developed analysis of null areas (ANA), an efficient method to calculate cavity volumes.

Intrinsically Disordered Region Modulates Ligand Binding in Glutaredoxin 1 from .

Glutaredoxins are small proteins that share a common well-conserved thioredoxin-fold and participate in a wide variety of biological processes. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (Fe-S) metabolism. In the present work, we report different structural and dynamics aspects of 1CGrx1 from the pathogenic parasite that differentiate it from other orthologues by the presence of a parasite-specific unstructured N-terminal extension whose role has not been fully elucidated yet.

Back-and-Forth Energy Transfer during Electronic Relaxation in a Chlorin-Perylene Dyad.

Donor-acceptor dyads represent a practical approach to tuning the photophysical properties of linear conjugated polymers in materials chemistry. Depending on the absorption wavelength, the acceptor and donor roles can be interchanged, and as such, the directionality of the energy transfer can be controlled. Herein, nonadiabatic excited state molecular dynamics simulations have been performed in an arylethylene-linked perylene-chlorin dyad.

Excitation Energy Transfer between bodipy Dyes in a Symmetric Molecular Excitonic Seesaw.

We examine the redistribution of energy between electronic and vibrational degrees of freedom that takes place between a π-conjugated oligomer, a phenylene-butadiynylene, and two identical boron-dipyrromethene (bodipy) end-caps using femtosecond transient absorption spectroscopy, single-molecule spectroscopy, and nonadiabatic excited-state molecular dynamics (NEXMD) modeling techniques. The molecular structure represents an excitonic seesaw in that the excitation energy on the oligomer backbone can migrate to either one end-cap or the other, but not to both. The NEXMD simulations closely reproduce the characteristic time scale for redistribution of electronic and vibrational energy of 2.

Monitoring molecular vibronic coherences in a bichromophoric molecule by ultrafast X-ray spectroscopy.

The role of quantum-mechanical coherences in the elementary photophysics of functional optoelectronic molecular materials is currently under active study. Designing and controlling stable coherences arising from concerted vibronic dynamics in organic chromophores is the key for numerous applications. Here, we present fundamental insight into the energy transfer properties of a rigid synthetic heterodimer that has been experimentally engineered to study coherences.