State-selective dissociative double ionization of CH3I and CH2I2 via I 4d core-hole states studied by multi-electron-ion coincidence spectroscopy.

The dissociative double ionization of CH3I and CH2I2 irradiated with extreme ultraviolet light at hv = 100 eV is investigated by multi-electron-ion coincidence spectroscopy using a magnetic bottle type electron spectrometer. The spin-orbit state-resolved Auger electron spectra for the I 4d core-hole states, (I 4d3/2)-1 and (I 4d5/2)-1, provide clear identifications of electronic states of CH3I2+ and CH2I22+. The dominant ion species produced after the double ionization correlate with the Auger electron energy, showing that different fragmentation pathways are open depending on the electronic states populated by the Auger decay. Theoretical calculations are performed to understand the fragmentation from the doubly charged states and the observed spin-orbit specificity in the Auger decay.

De novo generation of optically active small organic molecules using Monte Carlo tree search combined with recurrent neural network.

Optically active small organic molecules are computationally designed using the ChemTS python library developed by Tsuda and collaborators, which utilizes a combined Monte Carlo tree search (MCTS) and recurrent neural network model. Geometry optimization and excited-state calculations are performed for each generated molecule, following which the excitation energy and dissymmetry factors are computed to evaluate the score function in the MCTS process. Using this procedure, molecules not contained in existing databases are generated. Molecules having either high dissymmetry factors or high transition dipole strengths can be generated depending on the choice of the score function. In a single trajectory with 100,000 trials, mutually similar high-scoring molecules are generated frequently after the initial 15,000-20,000 trials. This indicates that it is better to sample high-scoring molecules from several trajectories having a modest number of trials each than from a single trajectory having a large number of trials.

Anisotropic Poisson Effect and Deformation-Induced Fluorescence Change of Elastic 9,10-Dibromoanthracene Single Crystals.

Elastic organic crystals have attracted considerable attention as next-generation flexible smart materials. However, the detailed information on both molecular packing change and macroscopic mechanical crystal deformations upon applied stress is still insufficient. Herein, we report that fluorescent single crystals of 9,10-dibromoanthracene are elastically bendable and stretchable, which allows a detailed investigation of the deformation behavior. We clearly observed a Poisson effect for the crystal, where the short axes (b and c-axes) of the crystal are contracted upon elongation along the long axis (a-axis). Moreover, we found that the Poisson's ratios along the b-axis and c-axis are largely different. Theoretical molecular simulation suggests that the tilting motion of the anthracene may be responsible for the large deformation along the c-axis. Spatially resolved photoluminescence (PL) measurement of the bent elastic crystals reveals that the PL spectra at the outer (elongated), central (neutral), and inner (contracted) sides are different from each other.

Inversion of Optical Activity in the Synthesis of Mercury Sulfide Nanoparticles: Role of Ligand Coordination.

Optical activity in inorganic colloidal materials was controlled through interactions of chiral molecules with the nanoparticle (NP) surface. An inversion of optical activity in the synthesis of mercury sulfide (HgS) NPs was demonstrated with an intrinsically chiral crystalline system in the presence of an identical chiral capping ligand. A continuous decrease in the positive first Cotton effect and an eventual reversal of CD profile were observed upon heating the aqueous solution of HgS NPs capped with N-acetyl-l-cysteine (Ac-l-Cys) at 80 °C. Ac-l-Cys afforded two bidentate coordination configurations with an almost mirror image of each other using the thiolate and either of carboxylate or acetyl-carbonyl groups on the HgS core. Experiment and calculation suggest that a shift in the distribution of the NP formation with energy in response to the combinations of ligand coordination structure and chiral crystalline surface is responsible for the inversion of optical activity.

Theoretical study on mesoscopic-size impurity effects in the charge separation process of organic photocells.

A bulk-heterojunction structure is often employed to develop high-performance organic photocells, in which the donor and acceptor regions are complexly intertwined. In such situations, mesoscopic-scale islands and peninsulas that compose the donor materials may be formed in the acceptor region. Alternatively, the donor region may extend deeply into the acceptor region. This yields mesoscopic-size impurities that can create obstacles in the charge separation (exciton dissociation) process of organic photocells and prevents the dissociation of excitons (electron-hole pairs). We previously reported on the effect of the cooperative behavior between the hot charge transfer (CT) state and the dimensional (entropy) effect on the charge separation process. In this paper, we discuss the mesoscopic-scale impurity effect on the charge separation process in PCBM acceptor models by considering the hot CT state and dimensional effects. In addition, we discuss atomic-scale effects such as molecular distortions and conformation changes using molecular dynamics (MD) simulations.

From Linear to Foldamer and Assembly: Hierarchical Transformation of a Coplanar Conjugated Polymer into a Microsphere.

Despite the coplanar structure, a conjugated alternating copolymer forms amorphous, well-defined microspheres without π-stacked crystalline domains. Here, we gain insights into the mechanism of how the coplanar conjugated polymer forms amorphous microspheres by means of spectroscopic studies on the assembly/disassembly processes. The difference of the spectral profiles of photoabsorption and photoluminescence with varying solvent/nonsolvent composition clarifies that stepwise assembly takes place through the microsphere formation; [1] intrapolymer linear-to-folding transformation upon diffusion of polar nonsolvent and [2] interpolymer assembly of the foldamers upon further addition of the nonsolvent to form microspheres. As shown in various biopolymers such as proteins and DNA, such stepwise folding and assembly behaviors of conjugated polymers from primary to secondary and tertiary structure open a new way to create transformable functional materials.

A Series of Layered Assemblies of Hydrogen-Bonded, Hexagonal Networks of C3-Symmetric π-Conjugated Molecules: A Potential Motif of Porous Organic Materials.

Hydrogen-bonded porous organic crystals are promising candidates for functional organic materials due to their easy construction and flexibility arising from reversible bond formation-dissociation. However, it still remains challenging to form porous materials with void spaces that are well-controlled in size, shape, and multiplicity because even well-designed porous frameworks often fail to generate pores within the crystal due to unexpected disruption of hydrogen bonding networks or interpenetration of the frameworks. Herein, we demonstrate that a series of C3-symmetric π-conjugated planar molecules (Tp, T12, T18, and Ex) with three 4,4'-dicarboxy-o-terphenyl moieties in their periphery can form robust hydrogen-bonded hexagonal networks (H-HexNets) with dual or triple pores and that the H-HexNets stack without interpenetration to yield a layered assembly of H-HexNet (LA-H-HexNet) with accessible volumes up to 59%. Specifically, LA-H-HexNets of Tp and T12 exhibit high crystallinity and permanent porosity after desolvation (activation): SABET = 788 and 557 m(2) g(-1), respectively, based on CO2 sorption at 195 K. We believe that the present design principle can be applied to construct a wide range of two-dimensional noncovalent organic frameworks (2D-nCOFs) and create a pathway to the development of a new class of highly porous functional materials.

Auger decay of molecular double core-hole and its satellite states: comparison of experiment and calculation.

Auger decay of the C(2)H(2) double core-hole (DCH) states, including the single-site DCH (C1s(-2)), two-site DCH (C1s(-1)C1s(-1)), and satellite (C1s(-2)π(-1)π∗(+1)) states, has been investigated experimentally using synchrotron radiation combined with multi-electron coincidence method, and theoretically with the assumption of the two-step sequential model for Auger decay of the DCH states. The theoretical calculations can reproduce the experimental two-dimensional Auger spectra of the C(2)H(2) single-site DCH and satellite decays, and allow to assign the peaks appearing in the spectra in terms of sequential two-electron vacancy creations in the occupied valence orbitals. In case of the one-dimensional Auger spectrum of the C(2)H(2) two-site DCH decay, the experimental and calculated results agree well, but assignment of peaks is difficult because the first and second Auger components overlap each other. The theoretical calculations on the Auger decay of the N(2) single-site DCH state, approximately considering the effect of nuclear motion, suggest that the nuclear motion, together with the highly repulsive potential energy curves of the final states, makes an important effect on the energy distribution of the Auger electrons emitted in the second Auger decay.

Interatomic relaxation effects in double core ionization of chain molecules.

Core vacancies created on opposite sides of a molecule operate against each other in polarizing the environment between them. Consequently, the relaxation energy associated with the simultaneous creation of these two core holes turns out to be smaller than the sum of the relaxation energies associated with each individual single core vacancy created independently. The corresponding residual, termed interatomic relaxation energy, is sensitive to the environment. In the present paper we explore how the interatomic relaxation energy depends on the length and type of carbon chains bridging two core ionized nitrile groups (-C≡N). We have uncovered several trends and discuss them with the help of simple electrostatic and quantum mechanical models. Namely, the absolute value of the interatomic relaxation energy depends strongly on the orbital hybridization in carbons being noticeably larger in conjugated chains (sp and sp(2) hybridizations) possessing highly mobile electrons in delocalized π-type orbitals than in saturated chains (sp(3) hybridization) where only σ bonds are available. The interatomic relaxation energy decreases monotonically with increasing chain length. The corresponding descent is determined by the energetics of the molecular bridge, in particular, by the HOMO-LUMO gap. The smallest HOMO-LUMO gap is found in molecules with the sp(2)-hybridized backbone. Here, the interatomic relaxation energy decreases slowest with the chain length.

Auger decay of molecular double core-hole state.

We report on theoretical Auger electron kinetic energy distribution originated from sequential two-step Auger decays of molecular double core-hole (DCH) state, using CH(4), NH(3), and H(2)CO molecules as representative examples. For CH(4) and NH(3) molecules, the DCH state has an empty 1s inner-shell orbital and its Auger spectrum has two well-separated components. One is originated from the 1st Auger transition from the DCH state to the triply ionized states with one core hole and two valence holes (CVV states) and the other is originated from the 2nd Auger transition from the CVV states to quadruply valence ionized (VVVV) states. Our result on the NH(3) Auger spectrum is consistent with the experimental spectrum of the DCH Auger decay observed recently [J. H. D. Eland, M. Tashiro, P. Linusson, M. Ehara, K. Ueda, and R. Feifel, Phys. Rev. Lett. 105, 213005 (2010)]. In contrast to CH(4) and NH(3) molecules, H(2)CO has four different DCH states with C1s(-2), O1s(-2), and C1s(-1)O1s(-1) (singlet and triplet) configurations, and its Auger spectrum has more complicated structure compared to the Auger spectra of CH(4) and NH(3) molecules. In the H(2)CO Auger spectra, the C1s(-1)O1s(-1) DCH → CVV Auger spectrum and the CVV → VVVV Auger spectrum overlap each other, which suggests that isolation of these Auger components may be difficult in experiment. The C1s(-2) and O1s(-2) DCH → CVV Auger components are separated from the other components in the H(2)CO Auger spectra and can be observed in experiment. Two-dimensional Auger spectrum, representing a probability of finding two Auger electrons at specific pair of energies, may be obtained by four-electron coincidence detection technique in experiment. Our calculation shows that this two-dimensional spectrum is useful in understanding contributions of CVV and VVVV states to the Auger decay of molecular DCH states.

Double-core-hole spectroscopy for chemical analysis with an intense X-ray femtosecond laser.

Theory predicts that double-core-hole (DCH) spectroscopy can provide a new powerful means of differentiating between similar chemical systems with a sensitivity not hitherto possible. Although DCH ionization on a single site in molecules was recently measured with double- and single-photon absorption, double-core holes with single vacancies on two different sites, allowing unambiguous chemical analysis, have remained elusive. Here we report that direct observation of double-core holes with single vacancies on two different sites produced via sequential two-photon absorption, using short, intense X-ray pulses from the Linac Coherent Light Source free-electron laser and compare it with theoretical modeling. The observation of DCH states, which exhibit a unique signature, and agreement with theory proves the feasibility of the method. Our findings exploit the ultrashort pulse duration of the free-electron laser to eject two core electrons on a time scale comparable to that of Auger decay and demonstrate possible future X-ray control of physical inner-shell processes.

Theoretical molecular double-core-hole spectroscopy of nucleobases.

Double-core-hole (DCH) spectra have been investigated for pyrimidine, purine, the RNA/DNA nucleobases, and formamide, using the density functional theory (DFT) method. DCH spectra of formamide were also examined by the complete-active-space self-consistent-field (CASSCF) method. All possible single- and two-site DCH (ssDCH and tsDCH) states of the nucleobases were calculated. The generalized relaxation energy and interatomic generalized relaxation energy were evaluated from the energy differences between ssDCH and single-core-hole (SCH) states and between tsDCH and SCH states, respectively. The generalized relaxation energy is correlated to natural bond orbital charge, whereas the interatomic generalized relaxation energy is correlated to the interatomic distance between the core holes at two sites. The present analysis using DCH spectroscopy demonstrates that the method is useful for the chemical analysis of large molecular systems.

Application of the R-matrix method to photoionization of molecules.

The R-matrix method has been used for theoretical calculation of electron collision with atoms and molecules for long years. The method was also formulated to treat photoionization process, however, its application has been mostly limited to photoionization of atoms. In this work, we implement the R-matrix method to treat molecular photoionization problem based on the UK R-matrix codes. This method can be used for diatomic as well as polyatomic molecules, with multiconfigurational description for electronic states of both target neutral molecule and product molecular ion. Test calculations were performed for valence electron photoionization of nitrogen (N(2)) as well as nitric oxide (NO) molecules. Calculated photoionization cross sections and asymmetry parameters agree reasonably well with the available experimental results, suggesting usefulness of the method for molecular photoionization.

Electron scattering from gas-phase glycine molecules.

Low-energy electron collisions with gas-phase glycine molecules have been studied using the fixed-nuclei R-matrix method based on state-averaged complete-active-space self-consistent-field orbitals. A total of 40 electronic states of neutral glycine, including 3s and 3p Rydberg excited states, are included in the R-matrix model. A large peak is observed in the A(") partial elastic cross section around 3.4 eV, which originates from the pi( *) shape resonance. In addition, many sharp narrow peaks coming from core excited resonances are seen in the elastic and inelastic cross sections at energies above 5 eV. Although the effect of the Rydberg orbitals on the elastic cross section is insignificant, these orbitals are crucial to represent core excited resonances in the inelastic cross sections. In previous experiments on dissociative electron attachment to gas-phase glycine, noticeable product ion peaks have been observed at electron collision energies around 1-2 and 5-10 eV. The resonance positions obtained in our calculations are generally close to these experimental results.

Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase.

Cytochrome c oxidase is a redox-driven proton pump that creates a membrane proton gradient responsible for driving ATP synthesis in aerobic cells. The crystal structure of the enzyme has been recently solved; however, the details of the mechanism of its proton pumping remain unknown. The enzyme internal water molecules play a key role in proton translocation through the enzyme. Here, we examine the thermodynamic properties of internal water in a hydrophobic cavity around the catalytic center of the enzyme. The crystal structure does not show any water molecules in this region; it is believed, however, that, since protons are delivered to the catalytic center, where the reduction of molecular oxygen occurs, at least some water molecules must be present there. The goal of the present study was to examine how many water molecules are present in the catalytic center cavity and why these water molecules are not observed in the crystal structure of the enzyme. The behavior of water molecules is discussed in the context of redox-coupled proton translocation in the enzyme.

The Huggins band of ozone: unambiguous electronic and vibrational assignment.

The Huggins band of ozone is investigated by means of exact dynamics calculations using a new (diabatic) potential energy surface for the (1)B(2) state. The remarkable agreement with the measured spectrum strongly suggests that the Huggins band is due to the two C(s) potential wells of the (1)B(2) state. The vibrational assignment, based on the nodal structure of wave functions, supports the most recent experimental assignment.