Molecular Dynamics of Excited State Intramolecular Charge Transfer in Solution by Coherent Nuclear Wave Packets.

Revealing a proper reaction coordinate in a chemical reaction is the key step towards elucidation of the molecular reaction dynamics. In this report, we investigated the dynamics of intramolecular charge transfer (ICT) of 8-aminopyrene-1,3,6-trisulfonic acid (APTS) occurring in the excited state by time-resolved fluorescence (TF) and TF spectra. Accurate reaction rates and rate-dependent nuclear wave packets in the product state allow detailed investigation of the molecular reaction dynamics. The ICT rate is solvent dependent: (34 fs)-1 , (87 fs)-1 , and (∞)-1 in water, formamide, and dimethylformamide, respectively. By recording spectra of the nuclear wave packets for different reaction rates, chemical species responsible for the emission spectra can be positively identified. The origin of the wave packets can be deduced from the amplitude change of the wave packets at different reaction rates, and the vibrational modes that are associated with the reaction coordinate could be identified. Theoretical calculations of the vibrational reorganization energies reproduce the experimental spectrum of the nuclear wave packets and corroborate the conclusions.

Electronic and Structural Dynamics of Dicyanoaurate Trimer in Excited State.

A trimer of dicyanoaurate has been studied as a model system of the covalent chemical bond formation. Here, we report the dynamics of dicyanoaurate trimer in water upon photoexcitation by femtosecond time-resolved luminescence (TL) and luminescence spectra at cyrogenic temperature. Temperature was varied as a means to control the medium flexibility as well as the population of isomers. A unique parallelism between the luminescence spectrum vs. time and vs. temperature was observed, which enables unambiguous luminescence band assignments and facilitates investigation of the dynamics. Upon photoexcitation to S1, intersystem crossing proceeds in an ultrafast manner within 20 fs due to the large spin-orbit coupling followed by a structural change from a loose bent to a tight linear form in 1.5 ps. Higher oligomerization occurs above the melting temperature. TL reveals a strong coherent excitation of the symmetric Au-Au stretching vibration at 74 cm-1 through the non-Condon effect.

Coherent intermolecular proton transfer in the acid-base reaction of excited state pyranine.

Detailed molecular dynamics simulations of an acid-base reaction have been the subject of extensive investigations. Here we report the excited state proton transfer dynamics of pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) in acetate buffer by time-resolved fluorescence (TF) and quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) simulations. High time resolution in TF and TF spectra measurements allows the acquisition of accurate reaction kinetics. Upon the photoexcitation of HPTS, the proton (deuterium) is transferred coherently to acetate in 60 fs (80 fs) for a contact pair of HPTS (DPTS) and acetate by a hydrogen bond, which comprises approximately 28% of the population. ESPT proceeds slowly on a picosecond time scale for the remaining HPTS as reported previously. Coherent wave packet motions of the reactant (acid) and the product (conjugate base) enable the acquisition of the vibrational spectra of excited states via TF (VETF). A comparison of the VETFs of the reactant and the product and the calculation of the Huang-Rhys factors (vibrational reorganization energies) identify the vibrational modes that actively participate in the coherent proton transfer. In particular, the 246 cm-1 vibrational mode, which consists of in-plane skeletal stretching motion, promotes the ESPT by transferring the donor oxygen towards the acceptor oxygen in acetate. QM/EFP MD simulations corroborate the experiment and provide molecular details of the ESPT.

Photophysical and structural investigation of a (Py)A-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes.

In this study, we found a (Py)A-modified adenine cluster (A-cluster), a minimum fluorescent unit for significant emission wavelength changes, and investigated its photophysical and structural properties. The basic A-cluster unit was an adenine-pentad duplex containing stacked (Py)A pairs in the center aligned in an antiparallel manner. Spectral analysis of the A-cluster revealed remarkable reddish fluorescence with a large Stokes shift (∼195 nm) and a long life-time constant (31 ns), originated from exciton states formed by (Py)A pairs and neighboring adenines. Structurally, the exciton state of the A-cluster exhibited unusually high stability, relative to that of other five-mismatched duplexes, as a result of stabilization through strong stacking interactions (zipper-like structure) of the mismatched A-A and (Py)A pairs, rather than through traditional Watson-Crick base pairing. These spectral and structural properties of the A-clusters were specific to the adenine bases and highly disturbed by introducing other bases (T, G, and especially C) or an abasic site into the A-cluster, whereas they were enhanced through synergistic effects in systems containing multiple A-clusters. As a minimum unit for these unique properties, finally, the A-cluster was exploited as a fluorescent probing system for specific nucleic acid sequences, such as miR-21, accompanying distinct fluorescence color changes from blue to red. These findings indicated the potential utility of the A-cluster as a part of fluorescent probes exhibiting clear signaling upon micro-environmental changes.

Scanning Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Conformational Dynamics of DNA Holliday Junction from Microsecond to Subsecond.

Single-molecule Förster resonance energy transfer (smFRET) is widely utilized to investigate the structural heterogeneity and dynamics of biomolecules. However, it has been difficult to simultaneously achieve a wide observation time window, a high structure resolution, and a high time resolution with the current smFRET methods. Herein, we introduce a new method utilizing two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) and surface immobilization techniques. This method, scanning 2D FLCS, enables us to examine the structural heterogeneity and dynamics of immobilized biomolecules on a time scale from microsecond to subsecond by slowly scanning the sample stage at the rate of ∼1 µm/s. Application to the DNA Holliday junction (HJ) complex under various [Mg2+] conditions demonstrates that scanning 2D FLCS enables tracking reaction kinetics from 25 µs to 30 ms with a time resolution as high as 1 µs. Furthermore, the high structure resolution of scanning 2D FLCS allows us to unveil the ensemble nature of each isomer state and the heterogeneity of the dynamics of the HJ.

Extraction of rapid kinetics from smFRET measurements using integrative detectors.

Hidden Markov models (HMMs) are used to learn single-molecule kinetics across a range of experimental techniques. By their construction, HMMs assume that single-molecule events occur on slower timescales than those of data acquisition. To move beyond that HMM limitation and allow for single-molecule events to occur on any timescale, we must treat single-molecule events in continuous time as they occur in nature. We propose a method to learn kinetic rates from single-molecule Förster resonance energy transfer (smFRET) data collected by integrative detectors, even if those rates exceed data acquisition rates. To achieve that, we exploit our recently proposed "hidden Markov jump process" (HMJP), with which we learn transition kinetics from parallel measurements in donor and acceptor channels. HMJPs generalize the HMM paradigm in two critical ways: (1) they deal with physical smFRET systems as they switch between conformational states in continuous time, and (2) they estimate transition rates between conformational states directly without having recourse to transition probabilities or assuming slow dynamics. Our continuous-time treatment learns the transition kinetics and photon emission rates for dynamic regimes that are inaccessible to HMMs, which treat system kinetics in discrete time. We validate our framework's robustness on simulated data and demonstrate its performance on experimental data from FRET-labeled Holliday junctions.

Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics.

Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.

Visualizing biofilm by targeting eDNA with long wavelength probe CDr15.

Detection of the biofilm of bacteria would be a counter strategy to detect hidden bacteria in their camouflage. Through unbiased screening of bacteria biofilm, we discovered a long wavelength probe CDr15 with extracellular DNA as the molecular target. CDr15 revealed a real-time geometric distribution of eDNA in a 3D bacterial colony.

Excited state intramolecular proton transfer dynamics of 1-hydroxy-2-acetonaphthone.

Excited state intramolecular proton transfer (ESIPT) of 1-hydroxy-2-acetonaphthone (HAN) has been in controversy, mainly because its Stokes shift is small compared to those of typical ESIPT molecules. We have investigated excited state dynamics of HAN by time-resolved fluorescence with a resolution high enough to record the nuclear wave packet motions in the excited state. Population dynamics of both the normal and tautomer forms were recorded together with the wave packet motions of the tautomer in the excited state, which confirm the ESIPT of HAN. The population dynamics of the normal and tautomer forms imply that the ESIPT dynamics is biphasic with two time constants <25 and 80 fs. Theoretical analysis of the vibrational modes of the tautomer excited impulsively reveals that major part of the change for the ESIPT reaction is on the naphthalene ring.

Effects of Gold-Nanoparticle Surface and Vertical Coverage by Conducting Polymer between Indium Tin Oxide and the Hole Transport Layer on Organic Light-Emitting Diodes.

The effect of varying degrees of surface and vertical coverage of gold nanoparticles (Au-NPs) by poly(styrenesulfonate)-doped poly(3,4-ethylenedioxythiophene) ( PEDOT: PSS), which was used as a capping layer between indium tin oxide (ITO) and a hole transport layer (HTL) on small-molecule fluorescent organic light-emitting diodes (OLEDs), was systemically investigated. With respect to the Au-NP loading amount and size, the resultant current densities influenced the charge balance and, therefore, the OLED device performance. When the capping layer consisted of ITO/Au-NPs/ PEDOT: PSS+Au-NPs, superior device performance was obtained with 10-nm Au-NPs through increased surface coverage in comparison to other Au-NP PEDOT:PSS coverage conditions. Furthermore, the Au-NP size determined the vertical coverage of the capping layer. The current densities of OLEDs containing small Au-NPs (less than 30 nm, small vertical coverage) covered by PEDOT: PSS decreased because of the suppression of the hole carriers by the Au-NP trapping sites. However, the current densities of the devices with large Au-NPs (over 30 nm, large vertical coverage) increased. The increased electromagnetic fields observed around relatively large Au-NPs under electrical bias were attributed to increased current densities in the OLEDs, as confirmed by the finite-difference time-domain simulation. These results show that the coverage conditions of the Au-NPs by the PEDOT: PSS clearly influenced the OLED current density and efficiency.