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Precise understanding of the electronic structures of optically dark triplet–triplet multiexcitons of π-conjugated carbon-based systems requires computations incorporating configuration interaction (CI) with up to quadruple excitations from the single-particle ground state of many-electron Hamiltonians. This continues to be a challenge in the context of intramolecular singlet fission (iSF), where the systems of interest are oligomers of large monomer molecules, and CI matrices have dimensions of several million. We have performed many-body calculations of the complete set of excited states relevant to iSF in Pentacene-(Tetracene)2-Pentacene oligomers, consisting of two terminal pentacene monomers linked by two tetracene monomers. Our computations within the Pariser–Parr–Pople Hamiltonian use an exciton basis that gives physical pictorial descriptions of all of the eigenstates. They are performed over an active space of twenty-eight monomer molecular orbitals and include configuration interaction with all relevant quadruple excitations within the active space, thereby ensuring high accuracy. We discuss the many-electron structures of the lowest optical predominantly intramonomer spin-singlets, intermonomer charge-transfer excitations, and most importantly, the complete set of low-energy covalent triplet–triplet multiexcitons. We can explain the weak binding energy of the pentacene-tetracene triplet–triplet eigenstate that is generated immediately following photoexcitation as opposed to the large binding energy of the triplet–triplet in polypentacene. Our approach allows calculations of excited state absorptions (ESAs) from the optical singlet as well as the triplet–triplet, thereby making comparisons with experimental transient absorption measurements in Pentacene-(Tetracene)2-Pentacene feasible. We explain the increase in lifetime with increasing numbers of tetracene monomers of the transient absorption associated with contiguous pentacene-tetracene triplet–triplet oligomers in this family of oligomers. We are able to give a pictorial description of the triplet separation following generation of the initial triplet–triplet, leading to a state with individual triplets occupying only the two pentacene monomers. We expect many applications of our theoretical approach to triplet separation in the iSF. 

We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on timescales faster than conformational transitions but describe a path of least resistance towards structural change. A key challenge is that harmonic approximations are ill-suited to characterize these vibrations, which are observed at far-infrared frequencies and are easily excited by thermal collisions at room temperature. Here, we approached this problem with a frequency-selective anharmonic (FRESEAN) mode analysis that does not rely on harmonic approximations and successfully isolates anharmonic low-frequency vibrations from short molecular dynamics simulation trajectories. We applied FRESEAN mode analysis to simulations of alanine dipeptide, a common test system for enhanced sampling simulation protocols, and compare the performance of isolated low-frequency vibrations to conventional user-defined collective variables (here backbone dihedral angles) in enhanced sampling simulations. The comparison shows that enhanced sampling along anharmonic low-frequency vibrations not only reproduces known conformational dynamics but can even further improve sampling of slow transitions compared to user-defined collective variables. Notably, free energy surfaces spanned by low-frequency anharmonic vibrational modes exhibit lower barriers associated with conformational transitions relative to representations in backbone dihedral space. We thus conclude that anharmonic low-frequency vibrations provide a promising path for highly effective and fully automated enhanced sampling simulations of conformational dynamics in biomolecules. 

Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist ininterfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors. 

We performed a time-resolved spectroscopy experiment on the dissociation of oxygen molecules after the interaction with intense extreme-ultraviolet (XUV) light from the free-electron laser in Hamburg at Deutsches Elektronen-Synchrotron. Using an XUV-pump/XUV-probe transient-absorption geometry with a split-and-delay unit, we observe the onset of electronic transitions in the O2+ cation near 50 eV photon energy, marking the end of the progression from a molecule to two isolated atoms. We observe two different time scales of 290 ± 53 and 180 ± 76 fs for the emergence of different ionic transitions, indicating different dissociation pathways taken by the departing oxygen atoms. With regard to the emerging opportunities of tuning the central frequencies of pump and probe pulses and of increasing the probe–pulse bandwidth, future pump–probe transient-absorption experiments are expected to provide a detailed view of the coupled nuclear and electronic dynamics during molecular dissociation. 

The yeast cytosine deaminase (yCD) enzyme/5-fluorocytosine prodrug system is a promising candidate for targeted chemotherapeutics. After conversion of the prodrug into the toxic chemotherapeutic drug, 5-fluorouracil (5-FU), the slow product release from the enzyme limits the overall catalytic efficiency of the enzyme/prodrug system. Here, we present a computational study of the product release of the anticancer drug, 5-FU, from yCD using metadynamics. We present a comparison of the 5-FU drug to the natural enzyme product, uracil. We use volume-based metadynamics to compute the free energy landscape for product release and show a modest binding affinity for the product to the enzyme, consistent with experiments. Next, we use infrequent metadynamics to estimate the unbiased release rate from Kramers time-dependent rate theory and find a favorable comparison to experiment with a slower rate of product release for the 5-FU system. Our work demonstrates how adaptive sampling methods can be used to study the protein−ligand unbinding process for engineering enzyme/prodrug systems and gives insights into the molecular mechanism of product release for the yCD/5-FU system. 

investigate photo-induced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photo-excitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an “associated” state, where the proton is “shared” between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a “solvent separated” state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a “water wire”) around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between emission wavelength and proton-HPTS distance over the simulations’ time scale, suggesting that emission wavelength can be used as a ruler for proton distance. Our simulations reveal that the “associated” state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized “solvent-separated” state) corresponds to the longest experimental time constant 

Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photo-induced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photo-excitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an “associated” state, where the proton is “shared” between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a “solvent separated” state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a “water wire”) around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between emission wavelength and proton-HPTS distance over the simulations’ time scale, suggesting that emission wavelength can be used as a ruler for proton distance. Our simulations reveal that the “associated” state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized “solvent-separated” state) corresponds to the longest experimental time constant. 

Soft polymer actuators are in increasing demand due to their more fluid like motion and flexibility when actuated than compared with rigid actuators, which makes them valuable in diverse engineering applications. One of the main types of soft polymer actuators is the dielectric elastomer actuator, whose working principle is to apply a voltage potential difference between electrodes to reduce the thickness of the elastomeric material while expanding its area. This paper looks at manufacturing a micro soft polymer dielectric elastomer actuator utilizing two-photon polymerization 3D printing. The actuator contains micro channels that are filled with an electrode by using capillary action. A complex helical geometry is designed, printed, and tested for electrode filling capabilities. Quite a few obstacles are described in this paper including the use of a newly released two-photon polymerization resin which has limited supporting resources, as well as the complex helical geometry having a large compliance that vastly complicates its fabrication, post-processing, handling, electrode filling, electrode integration, and actuation testing. However, these challenges are overcome by using the standard printing recipes currently available for the resins, adding electrode isolation layers, and printing thicker elastomer zones for more structural support. The results found solidify the approach of filling microchannels with electrodes through capillary action and lead to further the focus and creation of multi-functional micro soft actuators.