Dynamic Role of the Intramolecular Hydrogen Bonding in the S1 State Relaxation Dynamics Revealed by the Direct Measurement of the Mode-Dependent Internal Conversion Rate of 2-Chlorophenol and 2-Chlorothiophenol.

The dynamic role of the intramolecular hydrogen bond in the S1 relaxation of cis-2-chlorophenol (2-CP) or cis-2-chlorothiophenol (2-CTP) has been investigated in a state-specific manner. Whereas ultrafast internal conversion is dominant for 2-CP, the H-tunneling competes with internal conversion for 2-CTP even at the S1 origin. The S0-S1 internal conversion rate of 2-CTP could be directly measured from the S1 lifetimes of 2-CTP-d1 (Cl-C6H4-SD) as the D-tunneling is kinetically blocked, allowing distinct estimations of tunneling and internal conversion rates with increasing the energy. The internal conversion rate of 2-CTP increases by two times at the out-of-plane torsional mode excitation, suggesting that the internal conversion is facilitated at the nonplanar geometry. It then sharply increases at ∼600 cm-1, indicating that the S1/S0 conical intersection is readily accessible at the extended C-Cl bond length. The strength of the intramolecular hydrogen bond should be responsible for the distinct dynamic behaviors of 2-CP and 2-CTP.

Mode-dependent H atom tunneling dynamics of the S1 phenol is resolved by the simple topographic view of the potential energy surfaces along the conical intersection seam.

Mode-dependent H atom tunneling dynamics of the O-H bond predissociation of the S1 phenol has been theoretically analyzed. As the tunneling is governed by the complicated multi-dimensional potential energy surfaces that are dynamically shaped by the upper-lying S1(ππ*)/S2(πσ*) conical intersection, the mode-specific tunneling dynamics of phenol (S1) has been quite formidable to be understood. Herein, we have examined the topography of the potential energy surface along the particular S1 vibrational mode of interest at the nuclear configurations of the S1 minimum and S1/S2 conical intersection. The effective adiabatic tunneling barrier experienced by the reactive flux at the particular S1 vibrational mode excitation is then uniquely determined by the topographic shape of the potential energy surface extended along the conical intersection seam coordinate associated with the particular vibrational mode. The resultant multi-dimensional coupling of the specific vibrational mode to the tunneling coordinate is then reflected in the mode-dependent tunneling rate as well as nonadiabatic transition probability. Remarkably, the mode-specific experimental result of the S1 phenol tunneling reaction [K. C. Woo and S. K. Kim, J. Phys. Chem. A 123, 1529-1537 (2019)] (in terms of the qualitative and relative mode-dependent dynamic behavior) could be well rationalized by semi-classical calculations based on the mode-specific topography of the effective tunneling barrier, providing the clear conceptual insight that the skewed potential energy surfaces along the conical intersection seam (strongly or weakly coupled to the tunneling reaction coordinate) may dictate the tunneling dynamics in the proximity of the conical intersection.

πσ*-Mediated Nonadiabatic Tunneling Dynamics of Thiophenols in S1: The Semiclassical Approaches.

The S-H bond tunneling predissociation dynamics of thiophenol and its ortho-substituted derivatives (2-fluorothiophenol, 2-methoxythiophenol, and 2-chlorothiphenol) in S1 (ππ*) where the H atom tunneling is mediated by the nearby S2 (πσ*) state (which is repulsive along the S-H bond extension coordinate) have been investigated in a state-specific way using the picosecond time-resolved pump-probe spectroscopy for the jet-cooled molecules. The effects of the specific vibrational mode excitations and the SH/SD substitutions on the S-H(D) bond rupture tunneling dynamics have been interrogated, giving deep insights into the multidimensional aspects of the S1/S2 conical intersection, which also shapes the underlying adiabatic tunneling potential energy surfaces (PESs). The semiclassical tunneling rate calculations based on the Wentzel-Kramers-Brillouin (WKB) approximation or Zhu-Nakamura (ZN) theory have been carried out based on the ab initio PESs calculated in the (one, two, or three) reduced dimensions to be compared with the experiment. Though the quantitative experimental results could not be reproduced satisfactorily by the present calculations, the qualitative trends among different molecules in terms of the behavior of the tunneling rate versus the (adiabatic) barrier height or the number of PES dimensions could be rationalized. Most interestingly, the H/D kinetic isotope effect observed in the tunneling rate could be much better explained by the ZN theory compared to the WKB approximation, indicating that the nonadiabatic coupling matrix elements should be invoked for understanding the tunneling dynamics taking place in the proximity of the conical intersection.

S1-State Decay Dynamics of Benzenediols (Catechol, Resorcinol, and Hydroquinone) and Their 1:1 Water Clusters.

The S1-state decaying rates of the three different benzenediols, catechol, resorcinol, and hydroquinone, and their 1:1 water clusters have been state-specifically measured using the picosecond time-resolved parent ion transients obtained by the pump (excitation) and probe (ionization) scheme. The S1 lifetime of catechol is found to be short, giving τ ∼ 5.9 ps at the zero-point level. This is ascribed to the H-atom detachment from the free OH moiety of the molecule. Consistent with a previous report (J. Phys. Chem. Lett. 2013, 4, 3819-3823), the S1 lifetime gets lengthened with low-frequency vibrational mode excitations, giving τ ∼ 9.0 ps for the 116 cm-1 band. The S1 lifetimes at the additional vibronic modes of catechol are newly measured, showing the nonnegligible mode-dependent fluctuations of the tunneling rate. When catechol is complexed with water, the S1 lifetime is enormously increased to τ ∼ 1.80 ns at the zero-point level while it shows an unusual dip at the intermolecular stretching mode excitation (τ ∼ 1.03 ns at 146 cm-1). Otherwise, it is shortened monotonically with increasing the internal energy, giving τ ∼ 0.67 ns for the 856 cm-1 band. Two different asymmetric or symmetric conformers of resorcinol give the respective S1 lifetimes of 4.5 or 6.3 ns at their zero-point levels according to the estimation from our transients taken within the temporal window of 0-2.7 ns. When resorcinol is 1:1 complexed with H2O, the S1 decaying rate is slightly accelerated for both conformers. The S1 lifetimes of trans and cis forms of hydroquinone are measured to be more or less same, giving τ ∼ 2.8 ns at the zero-point level. When H2O is complexed with hydroquinone, the S1 decaying process is facilitated for both conformers, slightly more efficiently for the cis conformer.

Femtosecond Wavepacket Dynamics Reveals the Molecular Structures in the Excited (S1) and Cationic (D0) States.

Molecular structures in the electronically excited (S1) and cationic (D0) states of 2-fluorothioanisole (2-FTA) have been precisely refined from the real-time dynamics of the femtosecond (fs) wavepacket prepared by the coherent excitation of the Franck-Condon active out-of-plane torsional modes in the S1 ← S0 transition at 285 nm. The simulation to reproduce the experiment in terms of the beating frequencies gives the nonplanar geometry of 2-FTA in S1, where the out-of-plane dihedral angle (φ) of the S-CH3 moiety is 51° with respect to the molecular plane. The behavior of the fs wavepacket in terms of the amplitudes and phases with the change of the probe (ionization) wavelength (λprobe = 300-330 nm) provides the otherwise veiled structure of the cationic D0 state. While the 2-FTA cation adopts the planar geometry (φ = 0°) at the global minimum, it is found to have a vertical minimum at φ ≈ 135° from the perspective of the D0 ← S1 vertical transition. Ab initio calculations support the experiment quite well although the simulation using the model potentials could improve the match with the experiment, giving the new interpretation for the previously disputed photoelectron spectroscopic results.

Improved spectral resolution of the femtosecond stimulated Raman spectroscopy achieved by the use of the 2nd-order diffraction method.

Prolongation of the picosecond Raman pump laser pulse in the femtosecond stimulated Raman spectroscopy (FSRS) setup is essential for achieving the high spectral resolution of the time-resolved vibrational Raman spectra. In this work, the 2nd-order diffraction has been firstly employed in the double-pass grating filter technique for realizing the FSRS setup with the sub-5 cm-1 spectral resolution. It has been experimentally demonstrated that our new FSRS setup gives rise to a highly-resolved Raman spectrum of the excited trans-stilbene, which is much improved from those reported in the literatures. The spectral resolution of the present FSRS system has been estimated to be the lowest value ever reported to date, giving Δν = 2.5 cm-1.

Conformer-Specific Tunneling Dynamics Dictated by the Seam Coordinate of the Conical Intersection.

The dynamic role of the conical intersection "seam" coordinate has been first revealed in the H fragmentation reaction of ortho(o)-cresol conformers. One of the (3N - 8) dimensional seam coordinates of the S1(ππ*)/S2(πσ*) conical intersection has been identified as the CH3 torsional potential function. The tunneling dynamics of the reactive flux is dictated by its nuclear layout with respect to the CH3 torsional angle, as the multidimensional tunneling barrier is dynamically shaped along the conical intersection seam. The effective tunneling-barrier weight-averaged over the quantum-mechanical probability along the CH3 torsional angle perfectly explains the experimental finding: the sharp variation of the tunneling rate ((700-400) ps-1) with the CH3 torsional mode excitations within the narrow (0-100 cm-1) energetic window. The much longer S1 lifetime of cis compared to trans is ascribed to the higher-lying S1/S2 conical intersection of the former. With the use of distinct lifetimes, vibronic bands of each conformer could be completely separated.

Real-Time Tunneling Dynamics through Adiabatic Potential Energy Surfaces Shaped by a Conical Intersection.

Dynamic shaping of the adiabatic tunneling barrier in the S-H bond extension coordinate of several ortho-substituted thiophenols has been found to be mediated by low-frequency out-of-plane vibrational modes, which are parallel to the coupling vector of the branching plane comprising the conical intersection. The S-H predissociation tunneling rate (k) measured when exciting to the S1 zero-point level of 2-methoxythiophenol (44 ps)-1 increases abruptly, to k ≈ (22 ps)-1, at the energy corresponding to excitation of the 152 cm-1 out-of-plane vibrational mode and then falls back to k ≈ (40 ps)-1 when the in-plane mode is excited at 282 cm-1. Similar resonance-like peaks in plots of S1 tunneling rate versus internal energy are observed when exciting the corresponding low-frequency out-of-plane modes in the S1 states of 2-fluorothiophenol and 2-chlorothiophenol. This experiment provides clear-cut evidence for dynamical "shaping" of the lower-lying adiabatic potential energy surfaces by the higher-lying conical intersection seam, which dictates the multidimensional tunneling dynamics.

Real-Time Observation of Fermi Resonances in the S1 State of Phenol.

Fermi resonances in the first electronically excited (S1) state of phenol have been observed in real time. Quantum beats associated with coherent superposition of Fermi resonant eigenstates are manifested as temporal oscillations of the ionization cross sections of which the amplitudes are strongly dependent on the total ionization energy. This indicates that coherently excited eigenstates are effectively decomposed into their zeroth-order states, providing the unique opportunity for the investigation of nonstationary state dynamics in real-time. Energy gaps (Δν̃) of eigenstates within the laser coherence width have been most precisely determined up to date, giving Δν̃ ∼ 3.302 ± 0.001 or 1.655 ± 0.001 cm-1 for the 11/4110b1 or 122/8a1 Fermi doublets, respectively. Dephasing rate suddenly increases as the S1 internal energy becomes above ∼1500 cm-1, revealing the important role of energy randomization dynamics during the H atom tunneling process of phenol in S1.

Mode-specific excited-state dynamics of N-methylpyrrole.

State-selective deactivation rates of N-methylpyrrole in the S1 state have been measured by using the picosecond pump-probe method. The S1 decay time leading to the N-CH3 bond dissociation is found to be strongly mode-dependent as manifested in both S1 decay and methyl-fragment growth dynamics. Time-resolved velocity-map ion images of the ˙CH3 fragment, as far as the fragment of the Gaussian-shaped high kinetic energy distribution is concerned, suggest that the N-CH3 cleavage reaction might occur through an intermediate. Sudden decrease of the S1 lifetime at ∼700 cm-1 above the S1 origin is accompanied by the fragmentation of the Boltzmann-type low kinetic energy distribution. The appearance rate of this low-kinetic energy fragment turns out to be quite slow to give τ∼ 5 ns compared to the S1 lifetime of ∼174 ps at the +806 cm-1 band, for instance, confirming previous findings that the S1 decay process starts to be overwhelmed by a new fast nonradiative transition in the corresponding excitation energy region. The lifetime at the S1 origin accessed by the two-photon absorption is firstly measured to give τ∼ 8 ns. Using one and two photon absoption processes, a number of S1 vibronic bands are identified to give mode-dependent lifetimes spanning an enormously wide temporal range of 8 ns-5 ps in the quite narrow excitation energy region of 0-1800 cm-1 above the S1 origin. Understanding of the N-methylpyrrole dynamics on multidimensional excited-state potential energy surfaces governing energy dissipating processes will get much benefit from our detailed mode-specific lifetime measurements.

Multidimensional H Atom Tunneling Dynamics of Phenol: Interplay between Vibrations and Tunneling.

Multidimensional facets of the hydrogen tunneling dynamics of phenol excited in S1 (ππ*) have been unraveled to give particular S1 vibronic states strongly coupled or actively decoupled to the O-H tunneling coordinate. Strong mode-dependent variation of the tunneling rate measured with picosecond lasers indicates that tunneling probability is extremely sensitive to low-frequency vibrational modes seemingly orthogonal to the O-H elongation coordinate unless the rate of energy randomization exceeds that of tunneling. The multidimensional nature of tunneling has also been manifested in efficient internal-to-translational energy transfers observed at S1 vibronic modes strongly coupled to the tunneling coordinate, giving insights into otherwise the formidable multidimensional map of tunneling process. The nonadiabatic bifurcation dynamics in the later stage of the chemical reaction has been disentangled by analyzing picosecond time-resolved product state distributions, resolving a long controversial issue regarding the origin of high or low kinetic energy component of the product translational energy distributions.

Piperonylic acid stimulates keratinocyte growth and survival by activating epidermal growth factor receptor (EGFR).

Epidermal growth factor (EGF) stimulates cell growth, proliferation, and survival. The biological benefits of EGF have been utilized in medical uses for improving wound healing as well as in today's skin cosmetics. EGF has been found in urine, saliva, milk, and plasma, but its efficient isolation remains a difficult task. With technical advances, recombinant protein purification technique has been used for EGF production. However, the recombinant EGF is still expensive and keeping it with stable activity is difficult to be used widely. Thus, a molecule that can mimic the EGF activity would be a useful alternative of EGF. Herein, we have discovered that a natural small molecule piperonylic acid shows EGF-like activity in HaCaT keratinocytes. Piperonylic acid induced EGF receptor (EGFR) activation and resulted in serial activation of the downstream modulators. The activated signaling pathway eventually up-regulated gene expression of egr-1, c-fos, c-jun, and c-myc, which are involved in cell growth and survival. Moreover, piperonylic acid showed promoting role in keratinocyte growth and survival from UVB-induced cellular damages. This study has revealed the EGF-like activity of piperonylic acid and proposed that the piperonylic acid could be a promising component for skin wound healing agents or cosmetic ingredient.

Real-Time Observation of Nonadiabatic Bifurcation Dynamics at a Conical Intersection.

Looking into temporal dynamics of the reactive flux that is precisely located at the well-characterized conical intersection has been one of chemists' longstanding goals. We report here real-time nonadiabatic bifurcation dynamics in the S-CH3 bond predissociation of thioanisole (C6H5SCH3) in the first electronically excited state (S1). It is found that two distinct adiabatic and nonadiabatic reaction pathways are activated simultaneously only when the vibronic state near the first conical intersection is optically accessed. Our time-resolved measurement of the product state distribution could separate two different dynamic channels unambiguously, unraveling the detailed dynamic mechanism of the nonadiabatic reaction taking place in the vicinity of the conical intersection. The nonadiabatic channel, where the reactive flux funnels through two consecutive conical intersections along the reaction coordinate, is found to be significantly faster than the adiabatic channel along the minimum energy reaction pathway. The kinetic energy release ratio and the nonadiabatic transition probability are found to be much higher for the nonadiabatic channel than those of the adiabatic channel, giving insights into the bifurcation dynamics occurring at the conical intersection.

Heterogeneous ribonucleoprotein R regulates arylalkylamine N-acetyltransferase synthesis via internal ribosomal entry site-mediated translation in a circadian manner.

Rhythmic arylalkylamine N-acetyltransferase (AANAT) synthesis is a prominent circadian-controlled response that occurs in most mammals. AANAT is the core enzyme in melatonin production; because melatonin participates in many physiological processes, the regulation of AANAT is an important research topic. In this study, we focused on the role of heterogeneous ribonucleoprotein R (hnRNP R) in the translation of AANAT. A novel RNA-binding protein hnRNP R widely interacted with the 5' untranslated region (UTR) of AANAT mRNA and contributed to translation through an internal ribosomal entry site (IRES). Fine-tuning of AANAT protein synthesis occurred in response to knockdown and overexpression of hnRNP R. Nocturnal elevation of AANAT protein was dependent on the rhythmic changes of hnRNP R, whose levels are elevated in the pineal gland during nighttime. Increases in hnRNP R additionally improved AANAT production in rat pinealocytes under norepinephrine (NE) treatment. These results suggest that cap-independent translation of AANAT mRNA plays a role in the rhythmic synthesis of melatonin through the recruitment of translational machinery to hnRNP R-bound AANAT mRNA.

Vibronic structures and dynamics of the predissociating dimethyl sulfide and its isotopomers (CH3SCH3, CD3SCD3, CH3SCD3) at the conical intersection.

Conical intersection seam comprised of crossing surfaces of two lowest excited states of dimethyl sulfide (DMS) has been directly accessed by the one-photon excitation from the ground equilibrium state. Since the S-C bond rupture takes place promptly, the molecular structure on the excited state effectively belongs to C(S) symmetry. Namely, excited states of 1(1)B1 and 1(1)A2 in C(2)V become 1(1)A'' and 2(1)A'' states in C(S), respectively, and the optical transition from the ground equilibrium state to the dissociating molecule at the conical intersection seam is symmetry-allowed to facilitate the nonadiabatic transition on the 2(1)A'' state, leading eventually to the CH3S + CH3 products. The dynamic study of DMS, in this sense, gives the great opportunity to unravel the vibronic structure of the conical intersection seam by the conventional one-photon excitation method. In this work, utilizing the photofragment excitation (PHOFEX) spectroscopic method, the vibronic structures of DMS and its isotope analogs (CD3SCD3, CH3SCD3) at the conical intersection seam have been revealed, providing accurate lifetimes and detailed dynamics associated with individual vibronic transitions. The lifetime of the excited DMS is estimated to be ~100 fs, indicating that the dissociation is complete within one single oscillation in the conical intersection region. It is also found that the symmetric CSC stretching mode is strongly coupled to the reaction coordinate, as manifested by our experimental finding that the fragmentation yield of the S-CD3 bond is enhanced compared to that of the S-CH3 bond in the CH3SCD3 dissociation reaction only when the CSC symmetric stretching vibrational mode is excited at the conical intersection region. This work demonstrates that the better understanding of the excited state could make the bond-selective chemistry into reality.

Rhythmic interaction between Period1 mRNA and hnRNP Q leads to circadian time-dependent translation.

The mouse PERIOD1 (mPER1) protein, along with other clock proteins, plays a crucial role in the maintenance of circadian rhythms. mPER1 also provides an important link between the circadian system and the cell cycle system. Here we show that the circadian expression of mPER1 is regulated by rhythmic translational control of mPer1 mRNA together with transcriptional modulation. This time-dependent translation was controlled by an internal ribosomal entry site (IRES) element in the 5' untranslated region (5'-UTR) of mPer1 mRNA along with the trans-acting factor mouse heterogeneous nuclear ribonucleoprotein Q (mhnRNP Q). Knockdown of mhnRNP Q caused a decrease in mPER1 levels and a slight delay in mPER1 expression without changing mRNA levels. The rate of IRES-mediated translation exhibits phase-dependent characteristics through rhythmic interactions between mPer1 mRNA and mhnRNP Q. Here, we demonstrate 5'-UTR-mediated rhythmic mPer1 translation and provide evidence for posttranscriptional regulation of the circadian rhythmicity of core clock genes.

hnRNP Q mediates a phase-dependent translation-coupled mRNA decay of mouse Period3.

Daily mRNA oscillations of circadian clock genes largely depend on transcriptional regulation. However, several lines of evidence highlight the critical role of post-transcriptional regulation in the oscillations of circadian mRNA oscillations. Clearly, variations in the mRNA decay rate lead to changes in the cycling profiles. However, the mechanisms controlling the mRNA stability of clock genes are not fully understood. Here we demonstrate that the turnover rate of mouse Period3 (mPer3) mRNA is dramatically changed in a circadian phase-dependent manner. Furthermore, the circadian regulation of mPer3 mRNA stability requires the cooperative function of 5'- and 3'-untranslated regions (UTRs). Heterogeneous nuclear ribonucleoprotein Q (hnRNP Q) binds to both 5'- and 3'-UTR and triggers enhancement of translation and acceleration of mRNA decay. We propose the phase-dependent translation coupled mRNA decay mediated by hnRNP Q as a new regulatory mechanism of the rhythmically regulated decay of mPer3 mRNA.

Modulation of exosome-mediated mRNA turnover by interaction of GTP-binding protein 1 (GTPBP1) with its target mRNAs.

Eukaryotic mRNA turnover is among most critical mechanisms that affect mRNA abundance and are regulated by mRNA-binding proteins and the cytoplasmic exosome. A functional protein, guanosine-triphosphate-binding protein 1 (GTPBP1), which associates with both the exosome and target mRNAs, was identified. The overexpression of GTPBP1 accelerated the target mRNA decay, whereas the reduction of the GTPBP1 expression with RNA interference stabilized the target mRNA. GTPBP1 has a putative guanosine-triphosphate (GTP)-binding domain, which is found in members of the G-protein family and Ski7p, a well-known core factor of the exosome-mediated mRNA turnover pathway in yeast. Analyses of protein interactions and mRNA decay demonstrated that GTPBP1 modulates mRNA degradation via GTP-binding-dependent target loading. Moreover, GTPBP1-knockout models displayed multiple mRNA decay defects, including elevated nocturnal levels of Aanat mRNA in pineal glands, and retarded degradation of TNF-α mRNA in lipopolysaccharide-treated splenocytes. The results of this study suggest that GTPBP1 is a regulator and adaptor of the exosome-mediated mRNA turnover pathway.

hnRNP Q and PTB modulate the circadian oscillation of mouse Rev-erb alpha via IRES-mediated translation.

The physiological and behavioral circadian rhythms of most creatures are controlled by a harmony of functional relationships between clock genes. In mammals, several core clock genes show rhythmic profiles of their mRNA and protein expression. Among them, Rev-erb α functions as a transcriptional repressor, affecting expression patterns of other clock genes. For the continuous and robust oscillation of the molecular clock system, the levels of Rev-erb α protein are expected to be tightly regulated with the correct timing. Here, we demonstrate that Rev-erb α has an internal ribosomal entry site (IRES) in its 5' untranslated region. Furthermore, we demonstrate that heterogeneous nuclear ribonucleoprotein Q and polypyrimidine tract-binding protein (PTB) modulate the IRES-mediated translation of Rev-erb α. We suggest that the rhythmic binding affinity of hnRNP Q to the Rev-erb α IRES and the change in PTB cytosolic levels lead to maintenance of the oscillation profile of the Rev-erb α protein.

Circadian amplitude of cryptochrome 1 is modulated by mRNA stability regulation via cytoplasmic hnRNP D oscillation.

The mammalian circadian rhythm is observed not only at the suprachiasmatic nucleus, a master pacemaker, but also throughout the peripheral tissues. Its conserved molecular basis has been thought to consist of intracellular transcriptional feedback loops of key clock genes. However, little is known about posttranscriptional regulation of these genes. In the present study, we investigated the role of the 3'-untranslated region (3'UTR) of the mouse cryptochrome 1 (mcry1) gene at the posttranscriptional level. Mature mcry1 mRNA has a 610-nucleotide 3'UTR and mediates its own degradation. The middle part of the 3'UTR contains a destabilizing cis-acting element. The deletion of this element led to a dramatic increase in mRNA stability, and heterogeneous nuclear ribonucleoprotein D (hnRNP D) was identified as an RNA binding protein responsible for this effect. Cytoplasmic hnRNP D levels displayed a pattern that was reciprocal to the mcry1 oscillation. Knockdown of hnRNP D stabilized mcry1 mRNA and resulted in enhancement of the oscillation amplitude and a slight delay of the phase. Our results suggest that hnRNP D plays a role as a fine regulator contributing to the mcry1 mRNA turnover rate and the modulation of circadian rhythm.