Mapping the emergence of molecular vibrations mediating bond formation.

Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C â†’ A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.

Stratum-Confined Solid-State Reaction (SC-SSR) toward Colloidal Silicon-Based Hollow Nanostructures for Bioapplications.

Silicon nanostructures (SiNSs) can provide multifaceted bioapplications; but preserving their subhundred nm size during high-temperature silica-to-silicon conversion is the major bottleneck. The SC-SSR utilizes an interior metal-silicide stratum space at a predetermined radial distance inside silica nanosphere to guide the magnesiothermic reduction reaction (MTR)-mediated synthesis of hollow and porous SiNSs. In depth mechanistic study explores solid-to-hollow transformation encompassing predefined radial boundary through the participation of metal-silicide species directing the in-situ formed Si-phase accumulation within the narrow stratum. Evolving thin-porous Si-shell remains well protected by the in-situ segregated MgO emerging as a protective cast against the heat-induced deformation and interparticle sintering. Retrieved hydrophilic SiNSs (<100 nm) can be conveniently processed in different biomedia as colloidal solutions and endocytosized inside cells as photoluminescence (PL)-based bioimaging probes. Inside the cell, rattle-like SiNSs encapsulated with Pd nanocrystals can function as biorthogonal nanoreactors to catalyze intracellular synthesis of probe molecules through C-C cross coupling reaction.

Slow solvation dynamics beyond dielectric relaxation by three-pulse photon echo peak shift.

The dynamics of a liquid and its coupling to a solute are crucial for a better understanding of chemical processes in the liquid phase. In isotropic and homogeneous solutions, the time-correlation function of a solute is expected to vanish over time due to the translational and diffusive motions of the solvent. The three-pulse photon echo peak shift (3PEPS) is a third-order nonlinear spectroscopy technique that records the time-correlation function of a solute molecule in a solution, including an offset (inhomogeneity). In this work, we utilized a diffractive optics-based 3PEPS apparatus to fully resolve the dynamics in liquids from femtoseconds to nanoseconds while varying the temperature in the range of 80-298 K and the probe solute molecules. Our observations reveal dynamics slower than the dielectric relaxation of n-alcohols, even at room temperature, consisting of a ∼0.5 ns time constant that persists below the melting points and a static component (offset) on a nanosecond timescale. Based on the experiments, we suggest that locally formed glass-like clusters in liquids can be responsible for the slow dynamics. Our results may provide new insights into the dynamics of liquids and related phenomena such as liquid-glass and liquid-liquid phase transitions.

Excited State Intramolecular Proton Transfer Dynamics of Derivatives of the Green Fluorescent Protein Chromophore.

Excited state intramolecular proton transfer (ESIPT) dynamics of the o-hydroxy analogs of the green fluorescent protein (GFP) chromophore have been investigated by time-resolved spectroscopies and theoretical calculations. These molecules comprise an excellent system to investigate the effect of electronic properties on the energetics and dynamics of ESIPT and to realize applications in photonics. Time-resolved fluorescence with high enough resolution was employed to record the dynamics and the nuclear wave packets in the excited product state exclusively in conjunction with quantum chemical methods. The ESIPT are ultrafast occurring in 30 fs for the compounds employed in this work. Although the ESIPT rates are not affected by the electronic properties of the substituents suggesting barrierless reaction, the energetics, their structures, subsequent dynamics following ESIPT, and possibly the product species are distinct. The results attest that fine tuning of the electronic properties of the compounds may modify the molecular dynamics of ESIPT and subsequent structural relaxation to achieve brighter emitters with broad tuning capabilities.

Coherent Vibrational Spectrum via Time-Resolved Fluorescence for Molecular Dynamics and Identification of Emitting Species-Application to Excited-State Intramolecular Proton Transfer.

Time-resolved fluorescence (TF) with high-enough resolution enables recording of a coherent vibrational spectrum (CVS). Because a CVS attained via TF (CVSF) is descended from the frequency modulation of the fluorescence spectrum, it gives the vibrational spectrum of the emitting state. Therefore, CVSF can be a powerful tool for the identification of an emitting state along with the investigation of molecular dynamics in excited states. Herein, we report CVSF of a Schiff base salicylaldehyde azine (SAA) that has two possible excited-state intramolecular proton transfer (ESIPT) sites. The ESIPT time of SAA in dichloromethane is determined to be 22 fs. Quantitative agreement between the experimental CVSF and calculated CVSF of the mono-keto isomer demonstrates that ESIPT indeed occurs in SAA only on one side. More importantly, we show that a CVSF can be utilized to identify an emitting species and its state with the help of quantum chemical calculations. Implications of the CVSF obtained by assuming impulsive excitation of vibrations are discussed in terms of the molecular mechanism of ESIPT and the generation of nuclear wave packets in the product state.

Coherent internal conversion from high lying electronic states to S1 in boron-dipyrromethene derivatives.

Internal conversion is the first step after photoexcitation to high lying electronic states, and plays a central role in many photoinduced processes. In this report, we demonstrate a truly ultrafast internal conversion (IC) in large molecules by time-resolved fluorescence (TF). Following photoexcitation to the Sn (n ≥ 2) state, TF of the S1 state was recorded for two boron-dipyrromethene (BODIPY) derivatives in solution. IC to S1 takes place nearly instantaneously within 20 fs for both molecules. Abundant nuclear wave packet motions in the S1 state are manifest in the TF signals, which demonstrates that the IC in these BODIPY molecules is coherent with respect to most of the vibrational modes. Theoretical calculations assuming impulsive IC to S1 account for the wave packet dynamics accurately.

A solvent-solute cooperative mechanism for symmetry-breaking charge transfer.

Symmetry-breaking charge transfer (SBCT) is an important process at the early stages of the photoinduced processes in multichromophore systems such as the photosynthetic apparatus. We investigated the photoinduced SBCT dynamics of 9,9'-bianthracene (BA), a representative molecule showing SBCT, by time-resolved fluorescence (TF) with the highest time-resolution and excited-state quantum mechanics/effective fragment potential molecular dynamics (MD) simulation. TF experiments show that the SBCT kinetics matches quantitatively with the solvation function excluding the initial ultrafast component that is assigned to the inertial motion of the solvent. Therefore, it is established that the SBCT of BA is coupled solely with the rotational diffusion of solvent molecules excluding the inertial motion of solvents. MD simulations show that random rotational fluctuation of solvents mostly in the first solvation shell generates a transient electric field as high as 1.0 × 109 V m-1, which provides an asymmetric environment required for the generation of a CT state in this symmetric dimer. Once the CT state is formed, the dipole moment in the solute causes further rotation of solvent molecules leading to an augmented electric field, which in turn further stabilizes the CT state prohibiting the reverse reaction.

Role of coherent nuclear motion in the ultrafast intersystem crossing of ruthenium complexes.

Ultrafast intersystem crossing (ISC) in transition metal complexes leads to a long-lived active state with a high yield, which leads to efficient light energy conversion. The detailed mechanism of ISC may lead to a rational molecular design of superior transition metal complexes. Coherent nuclear wave packets observed in femtosecond time-resolved spectroscopies provide important information on the excited-state dynamics. In particular, analyzing the nuclear wave packets in both the reactant and the product may unveil the molecular dynamics of an ultrafast reaction. In this study, experimental evidence proving the reaction coordinates of the ultrafast ISC of ruthenium(ii) complexes is presented using coherent vibrational spectroscopy with a quantum chemical simulation of coherent vibrational motion. We observed vibrational modes strongly coupled to the ISC, whose vibrational coherences undergo remarkable attenuation after the ISC. The coupled modes contain metal-ligand stretching or symmetry breaking components, and the faster ISC rates of lower-symmetry ruthenium(ii) complexes support the significance of the latter.

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.

Excited-State Dynamics of Thioflavin T: Planar Stable Intermediate Revealed by Nuclear Wave Packet Spectroscopies.

Time-domain spectroscopies with time resolution shorter than the vibrational periods of interest were employed to reveal the reaction kinetics and molecular dynamics of the intramolecular charge transfer (ICT) reaction of thioflavin T in liquids. Time-resolved fluorescence spectra provided detailed reaction kinetics, and vibrational wave packets observed in the time-resolved fluorescence and transient absorption provided structural information on the reaction intermediate. Upon photoexcitation, the Franck-Condon state undergoes vibrational relaxation and minor conformational change to form a stable planar intermediate followed by the twisting of the central C-C single bond to form the twisted ICT state. The ICT reaction rate is determined by the solvent fluctuation excluding the inertial component in the solvation function.

Vibrational Spectrum of an Excited State and Huang-Rhys Factors by Coherent Wave Packets in Time-Resolved Fluorescence Spectroscopy.

Coherent nuclear wave packet motions in an electronic excited state of a molecule are measured directly by time-resolved spontaneous fluorescence spectroscopy with an unprecedented time resolution by using two-photon absorption excitation and fluorescence upconversion by noncollinear sum frequency generation. With an estimated time resolution of approximately 25 fs, wave packet motions of vibrational modes up to 1600 cm-1 are recorded for coumarin 153 in ethanol. Two-color transient absorption at 13 fs time resolution are measured to confirm the result. Vibrational displacements between the ground and excited states and Huang-Rhys factors (HRFs) are calculated by quantum mechanical methods and are compared with the experimental results. HRFs calculated by density functional theory (DFT) and time-dependent DFT reproduce the experiment adequately. This fluorescence-based method provides a unique and direct way to obtain the vibrational spectrum of a molecule in an electronic excited state and the HRFs, as well as the dynamics of excited states, and it might provide information on the structure of an excited state through the HRFs.

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.

Ultrafast generation of fundamental and multiple-order phonon excitations in highly enriched (6,5) single-wall carbon nanotubes.

Using a macroscopic ensemble of highly enriched (6,5) single-wall carbon nanotubes, combined with high signal-to-noise ratio and time-dependent differential transmission spectroscopy, we have generated vibrational modes in an ultrawide spectral range (10-3000 cm(-1)). A total of 14 modes were clearly resolved and identified, including fundamental modes of A, E1, and E2 symmetries and their combinational modes involving two and three phonons. Through comparison with continuous wave Raman spectra as well as calculations based on an extended tight-binding model, we were able to identify all the observed peaks and determine the frequencies of the individual and combined modes. We provide a full summary of phonon frequencies for (6,5) nanotubes that can serve as a basic reference with which to refine our understanding of nanotube phonon spectra as well as a testbed for new theoretical models.

Size-controlled soft-template synthesis of carbon nanodots toward versatile photoactive materials.

Size-controlled soft-template synthesis of carbon nanodots (CNDs) as novel photoactive materials is reported. The size of the CNDs can be controlled by regulating the amount of an emulsifier. As the size increases, the CNDs exhibit blue-shifted photoluminescence (PL) or so-called an inverse PL shift. Using time-correlated single photon counting, ultraviolet photoelectron spectroscopy, and low-temperature PL measurements, it is revealed that the CNDs are composed of sp² clusters with certain energy gaps and their oleylamine ligands act as auxochromes to reduce the energy gaps. This insight can provide a plausible explanation on the origin of the inverse PL shift which has been debatable over a past decade. To explore the potential of the CNDs as photoactive materials, several prototypes of CND-based optoelectronic devices, including multicolored light-emitting diodes and air-stable organic solar cells, are demonstrated. This study could shed light on future applications of the CNDs and further expedite the development of other related fields.

Retrieval of frequency spectrum from time-resolved spectroscopic data: comparison of Fourier transform and linear prediction methods.

Femtosecond time-resolved signals often display oscillations arising from the nuclear and electronic wave packet motions. Fourier power spectrum is generally used to retrieve the frequency spectrum. We have shown by numerical simulations and coherent phonon spectrum of single walled carbon nanotubes (SWCNT) that the Fourier power spectrum may not be appropriate to obtain the spectrum, when the peaks overlap with varying phases. Linear prediction singular value decomposition (LPSVD) can be a good alternative for this case. We present a robust way to perform LPSVD analysis and demonstrate the method for the chirality assignment of SWCNT through the time-domain coherent phonon spectroscopy.

Identification of an emitting molecular species by time-resolved fluorescence applied to the excited state dynamics of pigment yellow 101.

Time-resolved fluorescence (TRF) with a resolution higher than the periods of vibrations may provide the vibrational spectrum of an emitting species by directly recording the vibrational wave packet motions in time. We applied high-resolution TRF to investigate the excited-state dynamics of pigment yellow 101 (P.Y.101). The TRF spectra of P.Y.101 in dichloromethane showed that upon photoexcitation of the enol isomer, dynamics occur in the S1 state to form a product in two time constants at 30 and 140 fs. TRF signals were modulated due to the vibrational wave packet motions in the excited states, which provided the vibrational spectra of the emitting species. Depending on the emission wavelength, two different vibrational spectra were evident. With the help of theoretical calculations, the two spectra were assigned to the enol and keto isomers of P.Y.101 in the S1 state, leading to the conclusion that P.Y.101 undergoes ultrafast excited-state intramolecular proton transfer (ESIPT) with a quantum yield close to 1. Visible-pump infrared-probe transient absorption spectra were recorded to corroborate this conclusion.

Coherent and homogeneous intramolecular charge-transfer dynamics of 1-tert-butyl-6-cyano-1,2,3,4-tetrahydroquinoline (NTC6), a rigid analogue of DMABN.

We report the intramolecular charge-transfer (ICT) dynamics of 1-tert-butyl-6-cyano-1,2,3,4-tetrahydroquinoline (NTC6), a planar analogue of 4-(dimethylamino)benzonitrile (DMABN), by using time-resolved fluorescence (TRF) and TRF spectra (TRFS). TRFS allow accurate determination of the ICT dynamics free from the spectral relaxation caused by the solvation and vibronic relaxation. For NTC6 in tetrahydrofuran (THF), the locally excited (LE) state is populated exclusively presumably via a conical intersection from the initial photoexcited S2 (La) state, and the LE state undergoes ICT single exponentially with a time constant of 1.8 ± 0.2 ps. In acetonitrile, however, both LE (22%) and ICT (78%) states are populated from the S2 state, and the population in the LE state undergoes ICT in 800 ± 100 fs. The ICT state undergoes further relaxation in 1.2 ps along the solvation and the intramolecular nuclear coordinates involving the rotation of the amino group to form a twisted ICT state. Coherent nuclear wave packet motions of 130 cm(-1), which can be assigned to the -C≡N group bending mode, were observed in the TRF of the reactant (LE) and product (ICT) states, indicating that the ICT reaction is partially coherent. Compared with DMABN, the ICT dynamics of NTC6 are quite homogeneous, and we speculated on the narrow conformational distribution of NTC6 in the ground state along the rotation of the amino group due to its rigid structure.