Theoretical Design and Synthesis of Caged Compounds Using X-Ray-Triggered Azo Bond Cleavage.

Caged compounds are frequently used in life science research. However, the light used to activate them is commonly absorbed and scattered by biological materials, limiting their use to basic research in cells or small animals. In contrast, hard X-rays exhibit high bio-permeability due to the difficulty of interacting with biological molecules. With the main goal of developing X-ray activatable caged compounds, azo compounds are designed and synthesized with a positive charge and long π-conjugated system to increase the reaction efficiency with hydrated electrons. The azo bonds in the designed compounds are selectively cleaved by X-ray, and the fluorescent substance Diethyl Rhodamine is released. Based on the results of experiments and quantum chemical calculations, azo bond cleavage is assumed to occur via a two-step process: a two-electron reduction of the azo bond followed by N─N bond cleavage. Cellular experiments also demonstrate that the azo bonds can be cleaved intracellularly. Thus, caged compounds that can be activated by an azo bond cleavage reaction promoted by X-ray are successfully generated.

Ultrafast Raman observation of the perpendicular intermediate phantom state of stilbene photoisomerization.

Trans-cis photoisomerization is generally described by a model in which the reaction proceeds via a common intermediate having a perpendicular conformation around the rotating bond, irrespective of from which isomer the reaction starts. Nevertheless, such an intermediate has yet to be identified unambiguously, and it is often called the 'phantom' state. Here we present the structural identification of the common, perpendicular intermediate of stilbene photoisomerization using ultrafast Raman spectroscopy. Our results reveal ultrafast birth and decay of an identical, short-lived transient that exhibits a vibrational signature characteristic of the perpendicular state upon photoexcitation of the trans and cis forms. In combination with ab initio molecular dynamics simulations, it is shown that the photoexcited trans and cis forms are funnelled off to the ground state through the same, perpendicular intermediate.

Ab initio molecular dynamics study of intersystem crossing dynamics for MH2 (M = Si, Ge, Sn, Pb) on spin-pure and spin-mixed potential energy surfaces.

Recently, surface-hopping ab initio molecular dynamics (SH-AIMD) simulations have come to be used to discuss the mechanisms and dynamics of excited-state chemical reactions, including internal conversion and intersystem crossing. In dynamics simulations involving intersystem crossing, there are two potential energy surfaces (PESs) governing the motion of nuclei: PES in a spin-pure state and PES in a spin-mixed state. The former gives wrong results for molecular systems with large spin-orbit coupling (SOC), while the latter requires a potential gradient that includes a change in SOC at each point, making the computational cost very high. In this study, we systematically investigate the extent to which the magnitude of SOC affects the results of the spin-pure state-based dynamics simulations for the hydride MH2 (M = Si, Ge, Sn, Pb) by performing SH-AIMD simulations based on spin-pure and spin-mixed states. It is clearly shown that spin-mixed state PESs are indispensable for the dynamics simulation of intersystem crossing in systems containing elements Sn and Pb from the fifth period onward. Furthermore, in addition to the widely used Tully's fewest switches (TFS) algorithm, the Zhu-Nakamura (ZN) global switching algorithm, which is computationally less expensive, is applied to SH for comparison. The results from TFS- and ZN-SH-AIMD methods are in qualitative agreement, suggesting that the less expensive ZN-SH-AIMD can be successfully utilized to investigate the dynamics of photochemical reactions based on quantum chemical calculations.

An energy decomposition and extrapolation scheme for evaluating electron transfer rate constants: a case study on electron self-exchange reactions of transition metal complexes.

A simple approach to the analysis of electron transfer (ET) reactions based on energy decomposition and extrapolation schemes is proposed. The present energy decomposition and extrapolation-based electron localization (EDEEL) method represents the diabatic energies for the initial and final states using the adiabatic energies of the donor and acceptor species and their complex. A scheme for the efficient estimation of ET rate constants is also proposed. EDEEL is semi-quantitative by directly evaluating the seam-of-crossing region of two diabatic potentials. In a numerical test, EDEEL successfully provided ET rate constants for electron self-exchange reactions of thirteen transition metal complexes with reasonable accuracy. In addition, its energy decomposition and extrapolation schemes provide all the energy values required for activation-strain model (ASM) analysis. The ASM analysis using EDEEL provided rational interpretations of the variation of the ET rate constants as a function of the transition metal complexes. These results suggest that EDEEL is useful for efficiently evaluating ET rate constants and obtaining a rational understanding of their magnitudes.

Designing main-group catalysts for low-temperature methane combustion by ozone.

The catalytic combustion of methane at a low temperature is becoming increasingly key to controlling unburned CH4 emissions from natural gas vehicles and power plants, although the low activity of benchmark platinum-group-metal catalysts hinders its broad application. Based on automated reaction route mapping, we explore main-group elements catalysts containing Si and Al for low-temperature CH4 combustion with ozone. Computational screening of the active site predicts that strong Brønsted acid sites are promising for methane combustion. We experimentally demonstrate that catalysts containing strong Bronsted acid sites exhibit improved CH4 conversion at 250 °C, correlating with the theoretical predictions. The main-group catalyst (proton-type beta zeolite) delivered a reaction rate that is 442 times higher than that of a benchmark catalyst (5 wt% Pd-loaded Al2O3) at 190 °C and exhibits higher tolerance to steam and SO2. Our strategy demonstrates the rational design of earth-abundant catalysts based on automated reaction route mapping.

Real-time observation of the Woodward-Hoffmann rule for 1,3-cyclohexadiene by femtosecond soft X-ray transient absorption.

The stereochemistry of pericyclic reactions is explained by orbital symmetry conservation, referred to as the Woodward-Hoffmann (WH) rule. Although this rule has been verified using the structures of reactants and products, the temporal evolution of the orbital symmetry during the reaction has not been clarified. Herein, we used femtosecond soft X-ray transient absorption spectroscopy to elucidate the thermal pericyclic reaction of 1,3-cyclohexadiene (CHD) molecules, i.e., their isomerization to 1,3,5-hexatriene. In the present experimental scheme, the ring-opening reaction is driven by the thermal vibrational energy induced by photoexcitation to the Rydberg states at 6.2 eV and subsequent femtosecond relaxation to the ground state of CHD molecules. The direction of the ring opening, which can be conrotatory or disrotatory, was the primary focus, and the WH rule predicts the disrotatory pathway in the thermal process. We observed the shifts in K-edge absorption of the carbon atom from the 1s orbital to vacant molecular orbitals around 285 eV at a delay between 340 and 600 fs. Furthermore, a theoretical investigation predicts that the shifts depend on the molecular structures along the reaction pathways and the observed shifts in induced absorption are attributed to the structural change in the disrotatory pathway. This confirms that the orbital symmetry is dynamically conserved in the ring-opening reaction of CHD molecules as predicted using the WH rule.

Ligand release from silicon phthalocyanine dyes triggered by X-ray irradiation.

Ligand release from silicon phthalocyanine (SiPc) dyes triggered by near-infrared (NIR) light is a key photochemical reaction involving caged compounds based on SiPc. Although NIR light is relatively permeable compared with visible light, this light can be attenuated by tissue absorption and scattering; therefore, using light to induce photochemical reactions deep inside the body is difficult. Herein, because X-rays are highly permeable and can produce radicals through the radiolysis of water, we investigated whether the axial ligands of SiPcs can be cleaved using X-ray irradiation. SiPcs with different axial ligands (alkoxy, siloxy, oxycarbonyl, and phenoxy groups) were irradiated with X-rays under hypoxic conditions. We found that the axial ligands were cleaved via reactions with hydrated electrons (e-aq), not OH radicals, generated from water in response to X-ray irradiation, and SiPc with alkoxy groups exhibited the highest cleavage efficiency. A quantitative investigation revealed that X-ray-induced axial ligand cleavage proceeds via a radical chain reaction. The reaction is expected to be applicable to the molecular design of X-ray-activatable functional molecules in the future.

A reaction route network for methanol decomposition on a Pt(111) surface.

A reaction route network for the decomposition reaction of methanol on a Pt(111) surface was constructed by using the artificial force-induced reaction (AFIR) method, which can search for reaction paths automatically and systematically. Then, the network was kinetically analyzed by applying the rate constant matrix contraction (RCMC) method. Specifically, the time hierarchy of the network, the time evolution of the population initially given to CH3 OH to the other species on the network, and the most favorable route from CH3 OH to major and minor products were investigated by the RCMC method. Consistently to previous studies, the major product on the network was CO+4H, and the most favorable route proceeded through the following steps: CH3 OH → CH2 OH+H → HCOH+2H → HCO+3H → CO+4H. Furthermore, paths to byproducts found on the network and their kinetic importance were discussed. The present procedure combining AFIR and RCMC was thus successful in explaining the title reaction without using any information on its product or the reaction mechanism.

Real-Time Probing of an Atmospheric Photochemical Reaction by Ultrashort Extreme Ultraviolet Pulses: Nitrous Acid Release from o-Nitrophenol.

Photolysis of o-nitrophenol, contained in brown carbon, is considered to be a major process for the generation of nitrous acid (HONO) in the atmosphere. In this Letter, we used time-resolved photoelectron spectroscopy with 29.5 eV probe pulses and ab initio calculations to disentangle all reaction steps from the excitation to the dissociation of HONO. After excitation, intersystem crossing to the triplet manifold follows ultrafast excited-state intramolecular hydrogen transfer, where the molecules deplanarizes and finally splits off HONO after 0.5-1 ps.

Chiral lanthanide lumino-glass for a circularly polarized light security device.

Artificial light plays an essential role in information technologies such as optical telecommunications, data storage, security features, and the display of information. Here, we show a chiral lanthanide lumino-glass with extra-large circularly polarized luminescence (CPL) for advanced photonic security device applications. The chiral lanthanide glass is composed of a europium complex with the chiral (+)-3-(trifluoroacetyl)camphor ligand and the achiral glass promoter tris(2,6-dimethoxyphenyl)phosphine oxide ligand. The glass phase transition behavior of the Eu(III) complex is characterized using differential scanning calorimetry. The transparent amorphous glass shows CPL with extra-large dissymmetry factor of gCPL = 1.2. The brightness of the lumino-glass is one thousand times larger than that of Eu(III) luminophores embedded in polymer films of the same thickness at a Eu(III) concentration of 1 mM. The application of the chiral lanthanide lumino-glass in an advanced security paint is demonstrated.

Computational searches for crystal structures of dioxides of group 14 elements (CO2, SiO2, GeO2) under ultrahigh pressure.

In this study, we focused on the effect of pressure on the crystal structures of dioxides of group 14 elements, i.e. SiO2, GeO2, and CO2. Systematic searches for their crystal structures using the artificial force induced reaction method generated 219 and 147, 102 and 63, and 148 and 76 structures for SiO2, GeO2, and CO2, respectively, at 1 and 106 atm. At 1 atm, cristobalite-like, quartz, anatase-like, and stishovite were stable structures for SiO2 and GeO2. At 106 atm, structures of stishovite and CaCl2 type were relatively stable for SiO2 and GeO2. At 1 atm of CO2, molecular crystals were the most stable, whereas, quartz-like and cristobalite-like structures were obtained as stable structures at 106 atm. We discuss these pressure dependent structural variations systematically using the obtained structural dataset.

Understanding CO oxidation on the Pt(111) surface based on a reaction route network.

Analysis of a reaction on a solid surface is an important task for understanding the catalytic reaction mechanism. In this study, we studied CO oxidation on the Pt(111) surface by using the artificial force induced reaction (AFIR) method. A systematic reaction path search was done, and the reaction route network was created. This network included not only bond rearrangement paths but also migration paths of adsorbed species. Then, the obtained network was analyzed using a kinetics method called rate constant matrix contraction (RCMC). It is found that the bottleneck of the overall reaction is the CO2 generation step from an adsorbed CO molecule and an O atom. This result is consistent with the Langmuir-Hinshelwood (LH) mechanism with O2 dissociation discussed in previous studies. The present procedure, i.e., construction of the reaction route network by the AFIR method followed by application of the RCMC kinetics method to the resultant reaction route network, was fully systematic and uncovered two aspects: the impact of the existence of multiple paths in each bond rearrangement step and an entropic contribution arising from short-range migration of adsorbed species.

Exploring potential crossing seams in periodic systems: Intersystem crossing pathways in the benzene crystal.

The intersystem crossing (ISC) pathways of triplet benzene molecules in a benzene crystal were investigated theoretically. A combination of the gradient projection (GP) method, which is a standard method for optimizing the crossing seam of two potential energy surfaces, and the single-component artificial-force-induced reaction (SC-AFIR) method (GP/SC-AFIR) was used. This is the first reported use of a GP/SC-AFIR calculation using a density functional theory calculation with periodic boundary conditions. A systematic search for the minimum-energy structures in the seams of crossing of the singlet (S0) and triplet (T1) potential energy surfaces (S0/T1-MESX structures) found 39 independent S0/T1-MESX structures. Energy barriers between the S0/T1-MESX and the stationary structure of the triplet state (T1-MIN) were computed, and then two competing ISC pathways were extracted; the calculated overall energy barrier to the intermolecular C-C-bonded type (SX3) and the out-of-plane bent C-H type (SX15) S0/T1-MESX structures from T1-MIN were 0.26 and 0.27 eV, respectively. The rate constants for SX3 and SX15 formation were estimated to be 5.07 × 108 and 2.17 × 108 s-1 (at 273 K), respectively, or 9.73 × 10-5 and 4.78 × 10-6 s-1 (at 77 K), respectively. At 273 K, which is close to the melting point of the benzene crystal (278.5 K), SX3 and SX15 are easily accessible from T1-MIN, and ISC could occur through the S0/T1-MESX points. By contrast, at 77 K, T1-MIN survives long enough for phosphorescence to compete with ISC.

Exploring radiative and nonradiative decay paths in indole, isoindole, quinoline, and isoquinoline.

Radiative and nonradiative decay paths from the first excited singlet electronic state (S1) in four heteroaromatics, indole, isoindole, quinoline, and isoquinoline, were systematically explored. Three decay processes, i.e., internal conversion (IC), intersystem crossing (ISC), and fluorescence emission (FE), were compared. Minimum energy conical intersection structures between the electronic ground and first excited states were investigated to determine the most preferred IC path. The minimum energy seam of crossing (MESX) geometries between S1 and the lowest-lying triplet states and the spin-orbit couplings at these MESX structures were computed to identify the most feasible ISC path. The oscillator strength was calculated at each S1 local minimum to reveal the contribution of the FE process. The calculations clearly showed that indole had the highest fluorescent quantum yield, consistent with the experimental data. The present calculations also explained other experimental properties of the heteroaromatics such as ISC quantum yields.

Implementation and performance of the artificial force induced reaction method in the GRRM17 program.

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Theoretical study on mechanism of the photochemical ligand substitution of fac-[Re(I)(bpy)(CO)3(PR3)](+) complex.

The mechanism of the CO ligand dissociation of fac-[Re(I)(bpy)(CO)3P(OMe)3](+) has theoretically been investigated, as the dominant process of the photochemical ligand substitution (PLS) reactions of fac-[Re(I)(bpy)(CO)3PR3](+), by using the (TD-)DFT method. The PLS reactivity can be determined by the topology of the T1 potential energy surface because the photoexcited complex is able to decay into the T1 state by internal conversions (through conical intersections) and intersystem crossings (via crossing seams) with sufficiently low energy barriers. The T1 state has a character of the metal-to-ligand charge-transfer ((3)MLCT) around the Franck-Condon region, and it changes to the metal-centered ((3)MC) state as the Re-CO bond is elongated and bent. The equatorial CO ligand has a much higher energy barrier to leave than that of the axial CO, so that the axial CO ligand selectively dissociates in the PLS reaction. The single-component artificial force induced reaction (SC-AFIR) search reveals the CO dissociation pathway in photostable fac-[Re(I)(bpy)(CO)3Cl]; however, the dissociation barrier on the T1 state is substantially higher than that in fac-[Re(I)(bpy)(CO)3PR3](+) and the minimum-energy seams of crossings (MESXs) are located before and below the barrier. The MESXs have also been searched in fac-[Re(I)(bpy)(CO)3PR3](+) and no MESXs were found before and below the barrier.

Ultrafast X-ray Scattering from Molecules.

We present a theoretical framework for the analysis of ultrafast X-ray scattering experiments using nonadiabatic quantum molecular dynamics simulations of photochemical dynamics. A detailed simulation of a pump-probe experiment in ethylene is used to examine the sensitivity of the scattering signal to simulation parameters. The results are robust with respect to the number of wavepackets included in the total expansion of the molecular wave function. Overall, the calculated scattering signals correlate closely with the dynamics of the molecule.

From the (1B) Spectroscopic State to the Photochemical Product of the Ultrafast Ring-Opening of 1,3-Cyclohexadiene: A Spectral Observation of the Complete Reaction Path.

All stages of the electrocyclic ring-opening of 1,3-cyclohexadiene (CHD) were observed by time-resolved photoionization-photoelectron spectroscopy. Spectra of the 1B state, previously unobserved using time-resolved methods, were obtained upon optical excitation using ultrashort laser pulses at 4.60 or 4.65 eV, followed by ionization with pulses at 3.81, 3.85, and 4.10 eV, revealing a 1B lifetime of 30 fs. In an experiment using 3.07 eV probe photons and a 4.69 eV pump, we observed a time-sequenced progression of Rydberg states that includes s, p, and d states of the series n = 3 to 6. The sequentiality of the Rydberg signals points to an ionization mechanism that captures the molecule on different points along the reaction path in 2A. A dynamic fit of the Rydberg signals, coupled with MS-CASPT2 calculations, reveals that as the wavepacket moves down the potential energy surface it acquires kinetic energy at a rate of 28 eV/ps before reaching the conical intersection to the 1A ground state. During the reaction, the terminal carbon atoms separate at a speed of 16 Å/ps. A deconvolution of the Rydberg signals from a broad feature assigned to structurally disperse 1,3,5-hexatriene (HT) shows the formation of the open-chain hexatriene structure with an onset 142 fs after the initial absorption of a pump photon. The experimental observations are discussed in the context of recent ultrafast X-ray scattering experiments and theoretical quantum dynamics simulations.

Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging.

We report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropic component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.

Toward structural femtosecond chemical dynamics: imaging chemistry in space and time.

We aim to observe a chemical reaction in real time using gas-phase X-ray diffraction. In our initial experiment at the Linac Coherent Light Source (LCLS), we investigated the model system 1,3-cyclohexadiene (CHD) at very low vapor pressures. This reaction serves as a benchmark for numerous transformations in organic synthesis and natural product biology. Excitation of CHD by an ultraviolet optical pulse initiates an electrocyclic reaction that transforms the closed ring system into the open-chain structure of 1,3,5-hexatriene. We describe technical points of the experimental method and present first results. We also outline an approach to analyze the data involving nonlinear least-square optimization routines that match the experimental observations with predicted diffraction patterns calculated from trajectories for nonadiabatic vibronic wave packets.