Signature of the neighbor's quantum nuclear dynamics in the electron transfer mediated decay spectra.
Ontology highlight
ABSTRACT:
SUBMITTER: Ghosh A
PROVIDER: S-EPMC8278904 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The electron transfer (ET) dynamics from core/multi-shell (CdSe/CdS(3ML)ZnCdS(2ML)ZnS(2ML)) quantum dots (QDs) to adsorbed Fluorescein (F27) molecules have been studied by single particle spectroscopy to probe the relationship between single QD interfacial electron transfer and blinking dynamics. Electron transfer from the QD to F27 and the subsequent recombination were directly observed by ensemble-averaged transient absorption spectroscopy. Single QD-F27 complexes show correlated fluctuation of fluorescence intensity and lifetime, similar to those observed in free QDs. With increasing ET rate (controlled by F27-to-QD ratio), the lifetime of on states decreases and relative contribution of off states increases. It was shown that ET is active for QDs in on states, the excited state lifetime of which reflects the ET rate, whereas in the off state QD excitons decay by Auger relaxation and ET is not a competitive quenching pathway. Thus, the blinking dynamics of single QDs modulate their interfacial ET activity. Furthermore, interfacial ET provides an additional pathway for generating off states, leading to correlated single QD interfacial ET and blinking dynamics in QD-acceptor complexes. Because blinking is a general phenomenon of single QDs, it appears that the correlated interfacial ET and blinking and the resulting intermittent ET activity are general phenomena for single QDs.
| S-EPMC3170728 | biostudies-literature
Project description:Graphene quantum dots (GQDs) were connected to [Ru(bpy)3]2+ to sense DNA-mediated charge transfer. Interaction between abasic site double stranded DNA (Abasic-DNA) and [Ru(bpy)3-GQD]2+ was investigated by absorption spectroscopy, gel electrophoresis, circular dichroism, and melting temperature measurements. The results indicate that [Ru(bpy)3-GQD]2+ could be intercalated into double stranded DNA. Using [Ru(bpy)3-GQD]2+ as a signal molecule, the charge transfer performance of DNA-intercalated [Ru(bpy)3-GQD]2+ was determined using electrochemical and electrochemiluminescence measurements. Various DNA types were immobilized on Au electrodes via Au-S bonds. Electrochemiluminescence and electrochemical measurements indicate that [Ru(bpy)3-GQD]2+ could enhance DNA-mediated charge transfer when intercalated into an abasic site of double stranded DNA. And comparing with [Ru(bpy)3]2+, it can be concluded that GQDs intercalate into the DNA duplex by acting as a base analog, thus enhancing DNA charge transfer. These findings suggest that the DNA-GQD structure could aid the development of molecular devices and electric drivers, and broaden the application of DNA charge transfer.
| S-EPMC9072722 | biostudies-literature
Project description:We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule, a complex paradigmatic system in which the making and breaking of H-bonds in a highly anharmonic potential energy surface require a quantum mechanical treatment not only of the electrons but also of the nuclei. We combine density functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates but between 100 and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of 2.19 × 1011 s-1 at 150 K and 0.63 × 1011 s-1 at 100 K, in good agreement with experiment. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostated ring-polymer molecular dynamics simulations. The position and line shape of this peak, centered at around 2600 cm-1 and spanning 750 cm-1, stem from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to cis-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems.
| S-EPMC6728096 | biostudies-literature
Project description:Compound identification by mass spectrometry needs reference mass spectra. While there are over 102 million compounds in PubChem, less than 300,000 curated electron ionization (EI) mass spectra are available from NIST or MoNA mass spectral databases. Here, we test quantum chemistry methods (QCEIMS) to generate in silico EI mass spectra (MS) by combining molecular dynamics (MD) with statistical methods. To test the accuracy of predictions, in silico mass spectra of 451 small molecules were generated and compared to experimental spectra from the NIST 17 mass spectral library. The compounds covered 43 chemical classes, ranging up to 358 Da. Organic oxygen compounds had a lower matching accuracy, while computation time exponentially increased with molecular size. The parameter space was probed to increase prediction accuracy including initial temperatures, the number of MD trajectories and impact excess energy (IEE). Conformational flexibility was not correlated to the accuracy of predictions. Overall, QCEIMS can predict 70 eV electron ionization spectra of chemicals from first principles. Improved methods to calculate potential energy surfaces (PES) are still needed before QCEIMS mass spectra of novel molecules can be generated at large scale.
| S-EPMC7576811 | biostudies-literature
Project description:Theoretical prediction of electronic absorption spectra without input from experiments is no easy feat, as it requires addressing all of the factors that affect line shapes. In practice, however, the methodologies are limited to treat these ingredients only to a certain extent. Here, we present a multiscale protocol that addresses the temperature, solvent, and nuclear quantum effects as well as anharmonicity and the reconstruction of the final spectra from individual transitions. First, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics is conducted to obtain trajectories of solute-solvent configurations, from which the corresponding quantum-corrected ensembles are generated through the generalized smoothed trajectory analysis (GSTA). The optical spectra of the ensembles are then produced by calculating vertical transitions using time-dependent density-functional theory (TDDFT) with implicit solvation. To obtain the final spectral shapes, the stick spectra from TDDFT are convoluted with Gaussian kernels where the half-widths are determined by a statistically motivated strategy. We have tested our method by calculating the UV-vis spectra of a recently discovered acridine photocatalyst in two redox states. Vibronic progressions and broadenings due to the finite lifetime of the excited states are not included in the methodology yet. Nuclear quantization affects the relative peak intensities and widths, which is necessary to reproduce the experimental spectrum. We have also found that using only the optimized geometry of each molecule works surprisingly well if a proper empirical broadening factor is applied. This is explained by the rigidity of the conjugated chromophore moieties of the selected molecules, which are mainly responsible for the excitations in the spectra. In contrast, we have also shown that other parts of the molecules are flexible enough to feature anharmonicities that impair the use of other techniques such as Wigner sampling.
| S-EPMC8515811 | biostudies-literature
Project description:Biomolecular radiation damage is largely mediated by radicals and low-energy electrons formed by water ionization rather than by direct ionization of biomolecules. It was speculated that such an extensive, localized water ionization can be caused by ultrafast processes following excitation by core-level ionization of hydrated metal ions. In this model, ions relax via a cascade of local Auger-Meitner and, importantly, non-local charge- and energy-transfer processes involving the water environment. Here, we experimentally and theoretically show that, for solvated paradigmatic intermediate-mass Al3+ ions, electronic relaxation involves two sequential solute-solvent electron transfer-mediated decay processes. The electron transfer-mediated decay steps correspond to sequential relaxation from Al5+ to Al3+ accompanied by formation of four ionized water molecules and two low-energy electrons. Such charge multiplication and the generated highly reactive species are expected to initiate cascades of radical reactions.
| S-EPMC10533389 | biostudies-literature
Project description:Thermalization losses limit the photon-to-power conversion of solar cells at the high-energy side of the solar spectrum, as electrons quickly lose their energy relaxing to the band edge. Hot-electron transfer could reduce these losses. Here, we demonstrate fast and efficient hot-electron transfer between lead selenide and cadmium selenide quantum dots assembled in a quantum-dot heterojunction solid. In this system, the energy structure of the absorber material and of the electron extracting material can be easily tuned via a variation of quantum-dot size, allowing us to tailor the energetics of the transfer process for device applications. The efficiency of the transfer process increases with excitation energy as a result of the more favorable competition between hot-electron transfer and electron cooling. The experimental picture is supported by time-domain density functional theory calculations, showing that electron density is transferred from lead selenide to cadmium selenide quantum dots on the sub-picosecond timescale.
| S-EPMC5998019 | biostudies-literature
Project description:A switchable interaction between pairs of highly coherent qubits is a crucial ingredient for the physical realization of quantum information processing. One promising route to enable quantum logic operations involves the use of nuclear spins as protected elementary units of information, qubits. Here we propose a simple way to use fast electronic spin excitations to switch the effective interaction between nuclear spin qubits and the realization of a two-qubit molecular architecture based on highly coherent vanadyl moieties to implement quantum logic operations. Controlled generation of entanglement between qubits is possible here through chemically tuned magnetic coupling between electronic spins, which is clearly evidenced by the splitting of the vanadium(iv) hyperfine lines in the continuous-wave electron paramagnetic resonance spectrum. The system has been further characterized by pulsed electron paramagnetic resonance spectroscopy, evidencing remarkably long coherence times. The experimentally derived spin Hamiltonian parameters have been used to simulate the system dynamics under the sequence of pulses required to implement quantum gates in a realistic description that includes also the harmful effect of decoherence. This demonstrates the possibility of using this molecular complex to implement a control-Z (CZ) gate and simple quantum simulations. Indeed, we also propose a proof-of-principle experiment based on the simulation of the quantum tunneling of the magnetization in a S = 1 spin system.
| S-EPMC6062844 | biostudies-other
Project description:Ultrafast charge-transfer (i.e., electron and hole) dynamics has been investigated between the cesium lead bromide (CsPbBr3, CPB) perovskite nanocrystals (NCs) and cadmium selenide (CdSe) quantum dots (QDs) as a new composite material for photocatalytic and photovoltaic applications. The CPB NCs have been synthesized and characterized by high-resolution transmission electron microscopy (HR-TEM) and X-ray diffraction (XRD) pattern. The redox levels (i.e., conduction band (CB) and valence band (VB)) of the CPB NCs and CdSe QDs suggest the feasibility of photoexcited electron transfer from CPB NCs to CdSe QDs and photoexcited hole transfer from CdSe QDs to CPB NCs, and it has been confirmed by both steady-state and time-resolved spectroscopy. To investigate the electron- and hole-transfer dynamics in ultrafast time scale, we have performed femtosecond up-conversion and femtosecond transient absorption studies. The measured electron-transfer time from CPB NCs to CdSe QDs and hole-transfer time from CdSe QDs to CPB NCs were found to be 550 and 750 fs, respectively. Interestingly, the charge-transfer process found to be restricted in CPB/CdSe@CdS core-shell system where electron transfer from CPB NCs to core shell takes place, but the hole transfer from core shell to CPB NCs found to be restricted due to CdS shell making the process thermodynamically nonviable. Our observation has suggested that after the photoexcitation of CPB NCs/CdSe QDs composite system, a charge-separated state is formed where the electrons are localized in CB of CdSe QDs and holes are localized in VB of CPB NCs. This makes the composite system a better material for efficient light harvesting and photocatalytic material as compared to the individual ones.
| S-EPMC6641258 | biostudies-literature
Project description:Electron-transfer dissociation (ETD) induces fragmentation along the peptide backbone by transferring an electron from a radical anion to a protonated peptide. In contrast with collision-induced dissociation, side chains and modifications such as phosphorylation are left intact through the ETD process. Because the precursor charge state is an important input to MS/MS sequence database search tools, the ability to accurately determine the precursor charge is helpful for the identification process. Furthermore, because ETD can be applied to large, highly charged peptides, the need for accurate precursor charge state determination is magnified. Otherwise, each spectrum must be searched repeatedly using a large range of possible precursor charge states. To address this problem, we have developed an ETD charge state prediction tool based on support vector machine classifiers that is demonstrated to exhibit superior classification accuracy while minimizing the overall number of predicted charge states. The tool is freely available, open source, cross platform compatible, and demonstrated to perform well when compared with an existing charge state prediction tool. The program is available from http://code.google.com/p/etdz/.
| S-EPMC2966942 | biostudies-literature