Amidoxime-Containing Zr and Hf Atomic Layer Deposition Precursors for Metal Oxide Thin Films

In this article, we discuss the synthesis of eight novel zirconium and hafnium complexes containing amidoxime ligands as potential precursors for atomic layer deposition (ALD). Two amidoximes, viz., (E)-N'-hydroxy-N,N-dimethylacetimidamide (mdaoH) and (Z)-N'-hydroxy-N,N-dimethylpivalimidamide (tdaoH), along with their Zr and Hf homoleptic complexes, Zr(mdao)4 (1), Hf(mdao)4 (2), Zr(tdao)4 (3), and Hf(tdao)4 (4) were prepared. We further synthesized heteroleptic compounds with different physical properties by introducing cyclopentadienyl (Cp) ligand, namely, CpZr(mdao)3 (5), CpHf(mdao)3 (6), CpZr(tdao)3 (7), and CpHf(tdao)3 (8). Thermogravimetric analysis was used for the assessment of the evaporation characteristics of complexes 1, 2, 5, and 6, and it revealed multistep weight losses with high residues. On the other hand, the thermogravimetric analysis curves of complexes 3, 4, 7, and 8 comprising tdao ligands revealed single-step weight losses with moderate residues. Single-crystal X-ray diffraction studies of complexes 1, 3, and 7 showed that all of the complexes have monomeric molecular structures. Complex 7 exhibited a low melting point (75 °C), good volatility, and high thermal stability compared with other complexes. Therefore, an atomic layer deposition process for the growth of ZrO2 was developed by using ZrCp(tdao)3 (7) as a novel precursor.

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory

The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.

Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory

It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory: Multireference Advantages with the Practicality of Linear Response Theory

The density functional theory (DFT) and linear response (LR) time-dependent (TD)-DFT are of the utmost importance for routine computations. However, the single reference formulation of DFT suffers in the description of open-shell singlet systems such as diradicals and bond-breaking. LR-TDDFT, on the other hand, finds difficulties in the modeling of conical intersections, doubly excited states, and core-level excitations. In this Perspective, we demonstrate that many of these limitations can be overcome by recently developed mixed-reference (MR) spin-flip (SF)-TDDFT, providing an alternative yet accurate route for such challenging situations. Empowered by the practicality of the LR formalism, it is anticipated that MRSF-TDDFT can become one of the major workhorses for general routine tasks.

Development of Novel Focal Irradiation Tool for High-Precision Irradiation Using Clinical Brachytherapy System

PURPOSE/OBJECTIVE(S)

Several small animals, including mice, are used to conduct research on state-of-the-art radiation therapy techniques or treatment-related toxicity. However, it is difficult to conduct the focal irradiation to a shallow depth on small animals, because irradiation using LINAC has limitations in energy and field size. The purpose of this paper was to develop a focal irradiation tool for high-precision irradiation and to evaluate beam characteristics.

MATERIALS/METHODS

We designed the collimator of 1 mm diameter consisting of tungsten material for high-precision irradiation applied to the clinical brachytherapy system and the percent depth dose and horizontal profile were measured. We compared the depth dose and horizontal profile with 4 mm diameter SRS cone for 6 MV in LINAC. We measured the PDD and horizontal profile using EBT3 film for high-precision irradiation of 1 mm diameter using Ir-192 source. In case of 4 mm diameter, the beam was measured using edge detector. In addition, all measurements were compared with the results of planning tool simulation.

RESULTS

In case of focal irradiation tool, the maximum dose showed at the surface for both measurement and simulation, and 26% and 32% doses at 1 mm depth, respectively. In addition, FWHM at a 1 mm depth showed that high-precision irradiation was possible with measurement and simulation results of 1.86 and 1.28 mm. In case of LINAC, the maximum dose was showed at a depth of 1 cm and 0.8 cm in the measurement and simulation, respectively. Even if the smallest cone is used, the FWHM at a dmax depth was 4.0 mm in both simulation and measurement.

CONCLUSION

We overcame the limitation for energy and field size through the focal irradiation tool for high-precision irradiation. The focal irradiation tool enables high dose delivery to the shallow depth. In addition, small FWHM reduced dose delivery to the periphery at a specific depth and enabled accurate dose delivery. These results mean that the focal irradiation tool can be useful in small animal experiments that require accurate doses near the shallow depth.

High-performance strategies for the recent MRSF-TDDFT in GAMESS

Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios.

Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation

A multiscale scheme (MLMS: Multi-Level Multi-Scale) to predict the ion mobility (μ) of amorphous organic semiconductors is proposed, which was successfully applied to the hole mobility predictions of 14 organic systems. An inverse relationship between μ and reorganization energy is observed due to local polaronic distortions. Another moderate inverse correlation between μ and distribution of site energy change exists, representing the effects of geometric flexibility. The former and the latter represent the intramolecular and intermolecular geometric effects, respectively. In addition, a linear correlation between transfer coupling and μ is observed, showing the importance of orbital overlaps between monomers. Especially, the highest hole mobility of C6-2TTN is due to its large transfer coupling. On the other hand, another high hole mobility of CBP turned out to come from the high first neighbor density (ρ_FND) of its first self-solvation, emphasizing the proper description of amorphous structural configurations with a sufficiently large number of monomers. In general, systems with either unusually high transfer coupling or high first neighbor density can potentially have high μ regardless of geometric effects. Especially, the newly suggested design parameter, ρ_FND, is pointing to a new direction as opposed to the traditional π-conjugation strategy.

Single-Benzene Dual-Emitters Harness Excited-State Antiaromaticity for White Light Generation and Fluorescence Imaging

Molecular emitters simultaneously generating light at different wavelengths have wide applications. With a small molecule, however, it is challenging to realize two independent radiative pathways. We invented the first examples of dual-emissive single-benzene fluorophores (SBFs). Two emissive tautomers are generated by synthetic modulation of the hydrogen bond acidity, which opens up pathways for excited-state proton transfer. White light is produced by a delicate balance between the energy and intensity of the radiative decay from each tautomer. We show that the excited-state antiaromaticity of the benzene core itself dictates the proton movements driving the tautomer equilibrium. Using this simple benzene platform, a fluorinated SBF was synthesized with a record high solubility in perfluorocarbon solvents. White light-emitting devices and multicolor imaging of perfluorocarbon nanodroplets in live cells demonstrate the practical utility of these molecules.

Accurate Spin-Orbit Coupling by Relativistic Mixed-Reference Spin-Flip-TDDFT

Relativistic mixed-reference spin-flip (MRSF)-TDDFT is developed considering the spin-orbit coupling (SOC) within the mean-field approximation. The resulting SOC-MRSF faithfully reproduces the experiments with very high accuracy, which is also consistent with the values by four-component (4c) relativistic CASSCF and 4c-CASPT2 in the spin-orbit-energy splitting calculations of the C, Si, and Ge atoms. Even for the fifth-row element Sn, the SOC-MRSF yielded accurate splittings (∼ 3 % error). In the SOC calculations of the molecular 4-thiothymine with a third-row element, SOC-MRSF values are in excellent agreement with those of the SO-GMC-QDPT2 level, regardless of geometries and exchange-correlation functionals. The same SOC-MRSF predicted the anticipated chance of S₁ (nπ*) → T₁ (ππ*) intersystem crossing, even in thymine with only second-row elements. With its accuracy and practicality, thus, SOC-MRSF is a promising electronic structure protocol in challenging situations such as nonadiabatic molecular dynamics (NAMD) incorporating both internal conversions and intersystem crossings in large systems.

Prototropically Controlled Dynamics of Cytosine Photodecay

The effect of the existence of several prototropic tautomers of cytosine on its UV/vis spectra and the excited state decay dynamics is studied by spectral and nonadiabatic molecular dynamics (NAMD) simulations in connection with the mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Simulated UV/vis spectra provide a strong indication that the H3N keto-amino cytosine tautomer (the least anticipated species) may be present under experimental conditions. The NAMD simulations yield a wide range of excited state decay constants for various tautomers of cytosine, ranging from ∼1.3 ps for the biologically relevant H1N keto-amino tautomer to ∼0.1 ps for the keto-imino tautomer. The slowness of the H1N decay dynamics follows from the presence of a barrier on the excited state energy surface separating the Franck-Condon structure from the major decay funnel, the conical intersection seam. It is suggested that the experimentally observed photodecay dynamics may result from a combination of the decay processes of various tautomers (H3N in particular) present simultaneously under the experimental conditions.

Ultrafast Excited State Aromatization in Dihydroazulene

Excited-state aromatization dynamics in the photochemical ring opening of dihydroazulene (DHA) is investigated by nonadiabatic molecular dynamics simulations in connection with the mixed-reference spin-flip (MRSF)-TDDFT method. It is found that, in the main reaction channel, the ring opening occurs in the excited state in a sequence of steps with increasing aromaticity. The first stage lasting ca. 200 fs produces an 8π semiaromatic S₁ minimum (S_1, min) through an ultrafast damped bond length alternation (BLA) movement synchronized with a partial planarization of the cycloheptatriene ring. An additional ca. 200 fs are required to gain the vibrational energy needed to overcome a ring-opening transition state characterized by an enhanced Baird aromaticity. Unlike other BLA motions of ππ* state, it was shown that their damping is a characteristic feature of aromatic bond-equalization process. In addition, some minor channels of the reaction have also been discovered, where noticeably higher barriers of the S₁ non/antiaromatic transition structures must be surmounted. These anti-Baird channels led to reformation of DHA or other closed-ring products. The observed competition between the Baird and anti-Baird channels suggests that the quantum yield of photochemical products can be controllable by tipping their balance. Hence, here we suggest including the concept of anti-Baird, which would expand the applicability of Baird rule to much broader situations.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory for Accurate X-ray Absorption Spectroscopy

It is demonstrated that the challenging core-hole particle (CHP) orbital relaxation for core electron spectra can be readily achieved by the mixed-reference spin-flip (MRSF)-time-dependent density functional theory (TDDFT). With the additional scalar relativistic effects on K-edge excitation energies of 24 second- and 17 third-row molecules, the particular ΔCHP-MRSF(R) exhibited near perfect predictions with RMSE ∼0.5 eV, featuring a median value of 0.3 and an interquartile range of 0.4. Overall, the CHP effect is 2-4 times stronger than relativistic ones, contributing more than 20 eV in the cases of sulfur and chlorine third-row atoms. Such high precision allows to explain the splitting and spectral shapes of O, N, and C atom K-edges in the ground state of thymine with atom as well as orbital specific accuracy. The same protocol with a double hole particle relaxation also produced remarkably accurate K-edge spectra of core to valence hole excitation energies from the first (n_O8π*) and second (ππ*) excited states of thymine, confirming the assignment of 1s → n excitation for the experimentally observed 526.4 eV peak. Regarding both accuracy and practicality, therefore, MRSF-TDDFT provides a promising protocol for core electron spectra of both ground and excited electronic states alike.

A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.

Accelerated Deep Learning Dynamics for Atomic Layer Deposition of Al(Me)3 and Water on OH/Si(111)

Knowledge of the detailed mechanism behind the atomic layer deposition (ALD) can greatly facilitate the optimization of the manufacturing process. Computational modeling can potentially foster the understanding; however, the presently available capabilities of the accurate ab initio computational techniques preclude their application to modeling surface processes occurring on a long time scale, such as ALD. Although the situation can be greatly improved using machine learning (ML), this technique requires an enormous amount of data for training datasets. Here, we propose an iterative protocol for optimizing ML training datasets and apply ML-assisted ab initio calculations to model surface reactions occurring during the Al(Me)₃/H₂O ALD process on the OH-terminated Si (111) surface. The protocol uses a recently developed low-dimensional projection technique (TDUS), greatly reducing the amount of information required to achieve high accuracy (ca. 1 kcal/mol or less) of the developed ML models. The resulting free energy landscapes reveal fine details of various aspects of the target ALD process, such as the surface proton transfer, zwitterionic surface configurations, elimination-addition/addition-elimination, and S_N2 reactions as well as the role of the surface entropic and temperature effects. Simulations of adsorption dynamics predict that the maximum physisorption rate of ca. 70% is achieved at the incidence velocity u_rms of the reactants in the range of 15-20 Å/ps. Hence, the proposed protocol furnishes a very effective tool to study complex chemical reaction dynamics at a much reduced computational cost.

Dicarbonyl anthracenes and phenanthrenes as singlet fission chromophores

Singlet fission is a highly desired process in photovoltaic devices as it can significantly enhance photoelectric conversion efficiency. Exploitation of this process in photovoltaics is hindered by the lack of appropriate chromophores. We used mixed-reference spin-flipping time-dependent density functional theory to investigate five di-carbonyl anthracenes and phenanthrenes, with the purpose to design singlet fission chromophores. Two molecules were found to be promising candidates. For all the dicarbonyl molecules, the oxygen lone pair orbitals were found to be involved in the excited states that are relevant to singlet fission.

Exploring Dyson's Orbitals and Their Electron Binding Energies for Conceptualizing Excited States from Response Methodology

The molecular orbital (MO) concept is a useful tool, which relates the molecular ground-state energy with the energies (and occupations) of the individual orbitals. However, analysis of the excited states from linear response computations is performed in terms of the initial state MOs or some other forms of orbitals, e.g., natural or natural transition orbitals. Because these orbitals lack the respective energies, they do not allow developing a consistent orbital picture of the excited states. Herein, we argue that Dyson's orbitals enable description of the response states compatible with the concepts of molecular orbital theory. The Dyson orbitals and their energies obtained by mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for the response ground state are remarkably similar to the canonical MOs obtained by the usual DFT calculation. For excited states, the Dyson orbitals provide a chemically sensible picture of the electronic transitions, thus bridging the chasm between orbital theory and response computations.

Internal Conversion between Bright (11Bu+) and Dark (21Ag-) States in s-trans-Butadiene and s-trans-Hexatriene

Internal conversion (IC) between the two lowest singlet excited states, 1¹B_u⁺ and 2¹A_g^-, of s-trans-butadiene and s-trans-hexatriene is investigated using a series of single- and multi- reference wave function and density functional theory (DFT) methodologies. Three independent types of the equation-of-motion coupled-cluster (EOMCC) theory capable of providing an accurate and balanced description of one- as well as two-electron transitions, abbreviated as δ-CR-EOMCC(2,3), DIP-EOMCC(4h2p){N_o}, and DEA-EOMCC(4p2h){N_u} or DEA-EOMCC(3p1h,4p2h){N_u}, consistently predict that the 1¹B_u⁺/2¹A_g^- crossing in both molecules occurs along the bond length alternation coordinate. However, the analogous 1¹B_u⁺ and 2¹A_g^- potentials obtained with some multireference approaches, such as CASSCF and MRCIS(D), as well as with the linear-response formulation of time-dependent DFT (TDDFT), do not cross. Hence, caution needs to be exercised when studying the low-lying singlet excited states of polyenes with conventional multiconfigurational methods and TDDFT. The multistate many-body perturbation theory methods, such as XMCQDPT2, do correctly reproduce the curve crossing. Among the simplest and least expensive computational methodologies, the DFT approaches that incorporate the contributions of doubly excited configurations, abbreviated as MRSF (mixed reference spin-flip) TDDFT and SSR(4,4), accurately reproduce our best EOMCC results. This is highly promising for nonadiabatic molecular dynamics simulations in larger systems.

Description of Sudden Polarization in the Excited Electronic States with an Ensemble Density Functional Theory Method

Sudden polarization (SP) is one of the manifestations of electron transfer in the electronically excited states of molecules. Proposed initially to explain the unusual reactivity of photoexcited olefins, SP often occurs in the excited states of molecules possessing strongly correlated diradical ground state. Theoretical description of SP involves mixing between the singly excited and the doubly excited zwitterionic states, which makes it inaccessible with the use of the popular linear-response time-dependent density functional theory methods. In this work, an extended variant of the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS, or SSR) method is applied to study SP in a number of organic diradical systems. To this end, the analytical derivative formalism is derived and implemented for the SSR(3,2) method (see the main text for explanation of the acronym), which enables the automatic geometry optimization and obtains the relaxed density matrices as well as the electron binding energies and respective Dyson's orbitals. Application of the new method to SP in the lowest singlet excited state of ethylene agrees with the results obtained previously with the use of multireference methods of wavefunction theory. A number of interesting manifestations of SP are observed, such as the charge transfer in photoexcited tetramethyleneethene (TME) diradical mediated by the vibrational motion and conductivity switching in the excited state of a donor-acceptor dyad placed in an external electric field.

Fast and Accurate Computation of Nonadiabatic Coupling Matrix Elements Using the Truncated Leibniz Formula and Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory

We present a fast and accurate numerical algorithm for computing the first-order nonadiabatic coupling matrix element (NACME). The algorithm employs the truncated Leibniz formula (TLF) approximation within the finite-difference method, which makes it easily applicable in connection with any wave function-based methodology. In this work, we used the algorithm in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT, MRSF for brevity). The accuracy is assessed for NACME between the singlet electronic states of a dissociating hydrogen molecule. It is demonstrated that an intermediate approximation, TLF(1), affords a negligible numeric error on the order of ∼10^-10 a.u. while enabling a fast computation of NACME. As the MRSF method yields the correct description of the dissociation curves of H₂ for all the electronic states involved, the numeric TLF(1)/MRSF NACME values are in excellent agreement with the reference analytical values obtained by the full configuration interaction. For polyatomic molecules, the MRSF NAC vectors agree very closely with the MRCISD NAC vectors. Hence, the proposed protocol is a promising tool for the evaluation of NACMEs.

Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine

Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S₁-trapping, S₂-trapping, and S₁&S₂-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S₂-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S₁-trapping mechanism with two lifetimes, τ₁ = 30 ± 1 fs and τ₂ = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S₂ (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S₂→S₁ internal conversion and resides around the minimum on the S₁ (n_Oπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S₂→S₁ internal conversion is mediated by fast bond length alternation distortion, the subsequent S₁→S₀ occurs through several conical intersections, involving a slow puckering motion.

How neutral nitrogen-containing compounds are oxidized in oxidative-denitrogenation of liquid fuel with TiO2@carbon

Oxidative-denitrogenation (ODN) of indole (IND) and methyl-substituted INDs (methyl-INDs), representative neutral nitrogen-containing compounds (NCCs), was carried out with TiO₂@C and H₂O₂ as heterogeneous catalyst and oxidant, respectively, under ultrasound irradiation. The oxidation of INDs progressed through radical formation, as evidenced by electron spin resonance and radical scavenger experiments. The oxidized position of INDs in the ODN process was checked via characterization of the obtained products. It was observed that the oxidation finally occurred on the carbon rather than on the nitrogen atom of INDs, unlike the oxidation of basic NCCs (e.g., oxidation on the nitrogen atom, as respective N-oxides were formed) and sulfur-containing compounds. To understand the relative reactivity and oxidation position, electron density (ED) on the nitrogen atom of the studied INDs and relative stability of representative intermediates/products were calculated. It could be confirmed that ED on the nitrogen atom of the INDs is very important in the oxidation of INDs since the ODN reactivity of INDs was enhanced with increasing ED on the nitrogen atom of the investigated INDs. Moreover, theoretical analyses of the relative stability of substrate and intermediates/products (especially for IND) can explain the route for the observed final products in ODN. In other words, oxygen on the nitrogen atom, obtained via the first step of oxidation (electrophilic addition of an active oxygen atom on nitrogen), moves to the nearby carbon atom, because of the relative stability of the intermediates and products.

Optimization of Three State Conical Intersections by Adaptive Penalty Function Algorithm in Connection with the Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory Method (MRSF-TDDFT)

A new adaptive algorithm for penalty function optimization for minimum-energy three-states conical intersections (ME3CI) is suggested. The new algorithm differs from the original penalty function algorithm by (a) removing the redundancy in the target function, (b) using an adaptive increment for the penalty function weighting factor, and (c) using tighter convergence criteria for the energy gap. The latter was introduced to guarantee convergence to a true conical intersection rather than to a narrowly avoided crossing geometry. The new algorithm was tested in the optimization of the ME3CI geometries in butadiene and malonaldehyde, where all of the previously found true ME3CI geometries were recovered. The previously found butadiene's CI_3/2/1 turned out to be a narrowly avoided crossing. For butadiene, seven new ME3CI geometries have been located. Because of the removal of the redundancy and the use of the adaptive weighting factor, the convergence rate of the new algorithm is noticeably improved as compared to that of the previously proposed penalty function algorithm. The application to malonaldehyde and butadiene demonstrates that the three-state conical intersections may be more abundant and hence more involved in the photochemistry than previously thought. The recently developed mixed-reference spin flip (MRSF)-TDDFT method yields ME3CI geometries and relative energies quantitatively consistent with the previously reported calculations at a much reduced computational cost.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory (MRSF-TDDFT) as a Simple yet Accurate Method for Diradicals and Diradicaloids

Due to their multiconfigurational nature featuring strong electron correlation, accurate description of diradicals and diradicaloids is a challenge for quantum chemical methods. The recently developed mixed-reference spin-flip (MRSF)-TDDFT method is capable of describing the multiconfigurational electronic states of these systems while avoiding the spin-contamination pitfalls of SF-TDDFT. Here, we apply MRSF-TDDFT to study the adiabatic singlet-triplet (ST) gaps in a series of well-known diradicals and diradicaloids. On average, MRSF displays a very high prediction accuracy of the adiabatic ST gaps with the mean absolute error (MAE) amounting to 0.14 eV. In addition, MRSF is capable of accurately describing the effect of the Jahn-Teller distortion occurring in the trimethylenemethane diradical, the violation of the Hund rule in a series of the didehydrotoluene diradicals, and the potential energy surfaces of the didehydrobenzene (benzyne) diradicals. A convenient criterion for distinguishing diradicals and diradicaloids is suggested on the basis of the easily obtainable quantities. In all of these cases, which are difficult for the conventional methods of density functional theory (DFT), MRSF shows results consistent with the experiment and the high-level ab initio computations. Hence, the present study documents the reliability and accuracy of MRSF and lays out the guidelines for its application to strongly correlated molecular systems.

Diboron- and Diaza-Doped Anthracenes and Phenanthrenes: Their Electronic Structures for Being Singlet Fission Chromophores

We used quantum chemistry methods at the levels of mixed-reference spin-flip time-dependent density functional theory and multireference perturbation theory to study diboron- and diaza-doped anthracenes and phenanthrenes. This class of structures recently surged as potential singlet fission chromophores. We studied electronic structures of their excited states and clarified the reasons why they satisfy or fail to satisfy the energy criteria for singlet fission chromophores. Many studied structures have their S₁ states not dominated by HOMO → LUMO excitation, so they cannot be described using the conventional two site model. This is attributed to frontier orbital energy shifts induced by the doping and different charge-transfer energies in different one-electron singlet excitations or, in other words, different polarizations of hole and/or particle orbitals in their S₁ and T₁ states. There is a mirror relation between the orbital energy shifts induced by diboron- and diaza-dopings, which together with alternant hydrocarbon pairings of occupied and unoccupied orbitals, leads to more mirror relations between the excited states of the two types of doped structures.

Computation of Molecular Electron Affinities Using an Ensemble Density Functional Theory Method

The computation of electron attachment energies (electron affinities) was implemented in connection with an ensemble density functional theory method, the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method. With the use of the extended Koopmans' theorem, the electron affinities and the respective Dyson orbitals are obtained directly for the neutral molecule, thus avoiding the necessity to compute the ionized system. Together with the EKT-SSR (extended Koopmans' theorem-SSR) method for ionization potentials, which was developed earlier, EKT-SSR for electron affinities completes the implementation of the EKT-SSR formalism, which can now be used for obtaining electron detachment as well as the electron attachment energies of molecules in the ground and excited electronic states. The extended EKT-SSR method was tested in the calculation of several closed-shell molecules. For the molecules in the ground states, the EKT-SSR energies of Dyson's orbitals are virtually identical to the energies of the unoccupied orbitals in the usual single-reference spin-restricted Kohn-Sham calculations. For the molecules in the excited states, EKT-SSR predicts an increase of the most positive electron affinity by approximately the amount of the vertical excitation energy. The electron affinities of a number of diradicals were calculated with EKT-SSR and compared with the available experimental data. With the use of a standard density functional (BH&HLYP), the EKT-SSR electron affinities deviate on average by ca. 0.2 eV from the experimental data. It is expected that the agreement with the experiment can be improved by designing density functionals parametrized for ionization energies.

Entangled iodine and hydrogen peroxide formation in ice

Ice-core records show that anthropogenic pollution has increased the global atmospheric concentrations of hydrogen peroxide and iodine since the mid-20th century. Here, for the first time, we demonstrate a highly efficient mechanism that synergistically produces them in icy water conditions. This reaction is aided by a key intermediate IO₂H, formed by an I^- ion with a dissolved O₂ in acidic icy water, which produces both I as well as O₂H radicals. I recombines with I^- to produce I₂^- at a diffusion-limited rate, followed by formation of I₃^- through disproportionation, while O₂H yields H₂O₂ with I^- and a proton dissolved in icy water.

Structural or population dynamics: what is revealed by the time-resolved photoelectron spectroscopy of 1,3-cyclohexadiene? A study with an ensemble density functional theory method

Time-resolved photoelectron spectra during the photochemical ring-opening reaction of 1,3-cyclohexadiene (CHD) are modeled by an ensemble density functional theory (eDFT) method. The computational methodology employed in this work is capable of correctly describing the multi-reference effects arising in the ground and excited electronic states of molecules, which is important for the correct description of the ring-opening reaction of CHD. The geometries of molecular species along the non-adiabatic molecular dynamics (NAMD) trajectories reported in a previous study of the CHD photochemical ring-opening were used in this work to calculate the ionization energies and the respective Dyson orbitals for all possible ionization channels. The obtained theoretical time-resolved spectra display decay characteristics in a reasonable agreement with the experimental observations; i.e., the decay (and rise) of the most mechanistically significant signals occurs on the timescale of 100-150 fs. This is very different from the excited state population decay characteristics (τ_S1 = 234 ± 8 fs) obtained in the previous NAMD study. The difference between the population decay and the decay of the photoelectron signal intensity is traced back to the geometric transformation that the molecule undergoes during the photoreaction. This demonstrates the importance of including the geometric information in interpretation of the experimental observations.

Computation of Molecular Ionization Energies Using an Ensemble Density Functional Theory Method

Computation of the ionization energies and of the respective Dyson orbitals based on the use of the extended Koopmans theorem (EKT) is implemented in connection with an ensemble density functional theory (eDFT) method, the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method. The new methodology enables fast computation of the ionization energies and evaluation of the respective Dyson orbitals, the square norms of which are related with the ionization probabilities, in the ground and excited electronic states of molecules. As the application of EKT recycles the intermediate quantities from the SSR analytical energy gradient, evaluation of the ionization energies and probabilities can be carried out on-the-fly during the nonadiabatic molecular dynamics simulations. This opens up a perspective for fast theoretical simulation of the time-resolved photoelectron spectroscopy observations. In the present work, the new methodology is tested in the computation of the ionization energies and Dyson orbitals of several molecules in the ground and excited electronic states, including strongly correlated species, such as the ozone molecule, dissociating chemical bonds, and conical intersections.

Low-dimensional projection approach for efficient sampling of molecular recognition and polymer aggregation

The one-dimensional projection (ODP) approach is extended to two-dimensional umbrella sampling (TDUS) and is applied to three different complex systems in combination with a reactive force field (ReaxFF). TDUS is capable of showing detailed features of the free-energy surface (FES) of the double-proton transfer of the acetic acid dimer. It also revealed the direct relationship between the types of hydrogen bonding and binding strengths in the case of adrenaline molecular recognition by SIVSF (Serine, Isoleucine, Valine, Cysteine, and Phenylalanine). The study of polymer aggregation using TDUS shows that aggregation is preferred with a less-polar solvent, which is also consistent with the experimental observation of a tape-casting process. Therefore, TDUS can be generally useful in FES explorations from simple chemical reactions to complex processes of molecular recognition and polymer aggregation.

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

Random rotational fluctuation of solvents generates a large transient electric field that breaks the symmetry required for symmetry breaking charge transfer.

Conical Intersections in Organic Molecules: Benchmarking Mixed-Reference Spin-Flip Time-Dependent DFT (MRSF-TD-DFT) vs Spin-Flip TD-DFT

The mixed-reference spin-flip time-dependent density functional theory (MRSF-TD-DFT) method eliminates the erroneous spin contamination of the SF-TD-DFT methodology, while retaining the conceptual and practical simplicity of the latter. The availability of the analytic gradient of the energy of the MRSF-TD-DFT response states enables automatic geometry optimization of the targeted states. Here, we apply the new method to optimize the geometry of several S₁/S₀ conical intersections occurring in typical organic molecules. We demonstrate that MRSF-TD-DFT is capable of producing the correct double-cone topology of the intersections and describing the geometry of the lowest-energy conical intersections and their relative energies with accuracy matching that of the best multireference wavefunction ab initio methods. In this regard, MRSF-TD-DFT differs from many popular single-reference methods, such as, e.g., the linear response TD-DFT method, which fail to produce the correct topology of the intersections. As the new methodology completely eliminates the ambiguity with the identification of the response states as proper singlets or triplets, which is plaguing the SF-TD-DFT calculations, it can be used for automatic geometry optimization and molecular dynamic simulations not requiring constant human intervention.

Design of singlet fission chromophores with cyclic (alkyl)(amino) carbene building blocks

We use MRSF-TDDFT and NEVPT2 methods to design singlet fission chromophores with the building blocks of cyclic (alkyl)(amino)carbenes (CAACs). CAAC dimers with C₂, C₄, and p-phenylene spacers are considered. The substitutions with trifluoromethyls and fluorine atoms at the α C position are investigated. The electronegative substituents enhance the π accepting capability of the α C while maintaining it as a quaternary C atom. The phenylene-connected dimers with the two substitutions are identified as promising candidates for singlet fission chromophores. The cylindrically symmetric C₂ and C₄ spacers allow for substantial structural reorganizations in the S₀-to-S₁ and S₀-to-T₁ excitations. Although the two substituted dimers with the C₄ spacer satisfy (or very close to satisfy) the primary thermodynamics criterion for singlet fission, the significant structural reorganizations result in high barriers so that the fission is kinetically unfavorable.

Time-dependent electron transfer rate between geminate ions with strong Coulomb interaction and distance-dependent reactivity

Previous analytic expressions for the time-dependent rate of diffusion-influenced electron-transfer between geminate ions were obtained for the case when the reaction occurs at a contact separation. By applying a recently developed solution method for the Fredholm integral equation of the second kind, we obtain an accurate analytic expression for the time-dependent electron-transfer rate with the account of the distance-dependent reactivity. We also consider the dependence of the rate on the initial separation between the geminate ions. We check the accuracy of the solution against numerical results obtained by solving the equation for the survival probability. The solution is found to be accurate enough for most reasonable parameter values.

Cryopreservation of Endangered Wild Species, Aster altaicus var. uchiyamae Kitam, Using Droplet-Vitrification Procedure

BACKGROUND

Aster altaicus var. uchiyamae Kitam is an endemic and endangered species in urgent need of a comprehensive conservation strategy.

OBJECTIVE

To develop an efficient cryopreservation protocol using in vitro shoot tips to complement traditional conservation approaches in case seeds are not available or insufficient for conservation programs.

METHODS

Shoot tips of in vitro plants were cryopreserved using a droplet-vitrification method following improvement of pre-culture, osmoprotection, vitrification solution (VS), unloading and post-culture treatments. The starting protocol included step-wise pre-culture with 10% and 17.5% sucrose for 55 h and 17 h, respectively, followed by osmoprotection with C4-35% (17.5% glycerol + 17.5% sucrose) for 30 min, and cryoprotection with B5-80% (40% glycerol + 40% sucrose) for 60 min.

RESULTS

Shoot tips of A. altaicus were found to be moderately sensitive to the osmotic stress. Pre-culture and osmoprotection were not critical for the regeneration of cryopreserved explants when either of these treatments was applied. Osmoprotection with C4-35% on ice for 60 min followed by cryoprotection with A3-80%, a modified and diluted PVS2, on ice for 60 min resulted in the highest (65.3%) regeneration of cryopreserved shoot tips. Among alternative VSs tested, A3-80% and B5-80% were superior to PVS2 and PVS3 used under the same conditions. Step-wise recovery of shoot tips on ammonium-free medium followed by GA₃-containing medium and medium without growth regulators were critical for the normal regeneration of both VS-treated and cryopreserved shoot tips.

CONCLUSIONS

Cryopreservation of in vitro shoot tips using droplet-vitrification was developed as a complementary conservation approach for A. altaicus. Adjustment of the composition of regrowth media depending on recovery stage was important for the regeneration of healthy plants from cryopreserved shoot tips.

Symmetry-breaking charge transfer dynamics of 9,9’-bianthracene revealed by experiment and theory

Symmetry-breaking charge transfer reaction of 9,9’-bianthracene is driven exclusively by the rotational fluctuation of solvents, not including the inertial component in the solvation dynamics. Torsional motion and bond shortening during the reaction were observed.

Design and photoisomerization dynamics of a new family of synthetic 2-stroke light driven molecular rotary motors

Synthetic 2-stroke light driven molecular rotary motors with ultrafast function and high quantum efficiency.

Theoretical modelling of the dynamics of primary photoprocess of cyclopropanone

Photodecomposition of cyclopropanone is investigated by static quantum chemical calculations and non-adiabatic molecular dynamics (NAMD) simulations.

Ligand-Specific Dissolution of Iron Oxides in Frozen Solutions

The freezing-enhanced dissolution of iron oxides by various ligands has been recently proposed as a new mechanism that may influence the supply of bioavailable iron in frozen environments. The ligand-induced dissolution of iron oxides is sensitively affected by the kind and concentration of ligands, pH, and kind of iron oxides. While most ligands are thought to be freeze-concentrated in the ice grain boundary region along with iron oxides to enhance the iron dissolution, this study found that some ligands, such as ascorbic acid, suppress the iron dissolution in frozen solution relative to that in aqueous solution. Such ligands are proposed to be preferentially incorporated in the ice lattice bulk and not freeze-concentrated in the liquid-like grain boundary. The experimental analysis estimated that the ionized forms of ligands (e.g., iodide ions) are hardly present in the ice bulk region (<3%) and enhance the iron dissolution in frozen solution (relative to that in aqueous solution), whereas some neutral ligands (e.g., undissociated ascorbic acid) are significantly trapped in the ice bulk (>50%) and suppress the iron dissolution compared to the aqueous counterpart. The present results reveal that the ligand-induced dissolution of iron oxide in frozen solution is not always enhanced relative to aqueous solution but depends upon the kind of ligand and experimental conditions.