Excitation configuration analysis for divide-and-conquer excited-state calculation method using dynamical polarizability.

The authors previously developed a divide-and-conquer (DC)-based non-local excited-state calculation method for large systems using dynamical polarizability [Nakai and Yoshikawa, J. Chem. Phys. 146, 124123 (2017)]. This method evaluates the excitation energies and oscillator strengths using information on the dynamical polarizability poles. This article proposes a novel analysis of the previously developed method to obtain further configuration information on excited states, including excitation and de-excitation coefficients of each excitation configuration. Numerical applications to simple molecules, such as ethylene, hydrogen molecule, ammonia, and pyridazine, confirmed that the proposed analysis could accurately reproduce the excitation and de-excitation coefficients. The combination with the DC scheme enables both the local and non-local excited states of large systems with an excited nature to be treated.

Factors governing the protonation of Keggin-type polyoxometalates: influence of the core structure in clusters.

Atomic substitution is a promising approach for controlling structures and properties for developing clusters with desired responses. Although many possible coordination candidates could be deduced for substitution, not all can be prepared. Therefore, predicting the correlation between structures and physical properties is important prior to synthesis. In this study, regarding Keggin-type polyoxometalates (POMs) as a model cluster, the dominant factors affecting the protonation were investigated by atomic substitutions and geometry changes. The valence of Keggin-type POMs and the constituent elements of the cluster shell structure affect the charge and potential distribution, which change the protonation sites. Furthermore, the valence of Keggin-type POMs and the bond length between the core and shell structure determine the protonation energy. These factors also affect the HOMO-LUMO gap, which governs photochemical and redox reactions. These governing factors derived from actual parameters of the α-isomer of Keggin-type POMs enabled us to deduce the protonation energy of the ß-isomer, which is more difficult to prepare and isolate than the α-isomer.

Range Separation Method for Density Functional Theory Based on Two-Electron Infinite-Order Two-Component Hamiltonian.

The range separation method for density functional theory (DFT) was extended to a two-component relativistic theory based on the unitary transformation of one- and two-electron operators and a density operator. In the framework of the spin-free infinite-order two-component Hamiltonian, we implemented several types of two-electron integrals of range-separated two-electron interactions arising from the unitary transformation. Numerical assessments were performed using long-range-corrected (LC)-DFT, which utilizes the range separation of an exchange functional. The present method successfully reproduced the reference values obtained by the four-component LC-DFT calculations when the whole unitary transformations of one-electron, full-range, and range-separated two-electron operators and a density operator were considered. An efficient scheme for the unitary transformation, which is termed the local unitary transformation (LUT), was also applied to the range-separated two-electron term and other operators. The LUT method reduced the computational costs of the LC-DFT calculations significantly without any loss of accuracy.

Comprehensive image dataset for enhancing object detection in chemical experiments.

The application of image recognition in chemical experiments has the potential to enhance experiment recording and risk management. However, the current scarcity of suitable benchmarking datasets restricts the applications of machine vision techniques in chemical experiments. This data article presents an image dataset featuring common chemical apparatuses and experimenter's hands. The images have been meticulously annotated, providing detailed information for precise object detection through deep learning methods. The images were captured from videos filmed in organic chemistry laboratories. This dataset comprises a total of 5078 images including diverse backgrounds and situations surrounding the objects. Detailed annotations are provided in accompanying text files. The dataset is organized into training, validation, and test subsets. Each subset is stored within independent folders for easy access and utilization.

Quantum mechanical assessment on the optical properties of capsanthin conformers.

As optical properties, the ultraviolet-visible (UV-Vis) absorption spectra of capsanthin-based red natural dye are a decisive parameter for their usage in various applications. Thus, accurately predicting the maximum UV-Vis wavelength ( λ max ) values is critical in designing dye-conjugated material. Extensive metadynamics simulations were carried out to generate capsanthin conformers at various levels of the extended tight-binding method. Benchmarking the time-dependent density-functional theory (TD-DFT) methods help understand the results of a particular functional and allows a comparison between results obtained with different functional. The long-range correction (LC) scheme in LC-TD-DFT-D4/ωB97X/def2-SVP has been found to reproduce the experimental λ max , and exhibited the effect of conformational changes to the calculated wavelengths. On the other hand, an inexpensive yet efficient LC-TD-DFTB method reproduced the experimental λ max insensitive to conformational changes.

Neutral-to-ionic photoinduced phase transition of tetrathiafulvalene-p-chloranil by electronic and vibrational excitation: A real-time nuclear-electronic dynamics simulation study.

Tetrathiafulvalene-p-chloranil exhibits photoinduced phase transition (PIPT) between neutral (N) and ionic (I) phases, in which the constituent molecules are approximately charge-neutral and ionic, respectively. In addition to visible-light irradiation, which can induce both N → I and I → N PIPTs, infrared irradiation has been reported to induce the N → I PIPT. These results suggest that N → I and I → N PIPTs can be driven by electronic excitation, and the I → N PIPT can also be driven by vibrational excitation. However, the feasibility of the N → I PIPT using vibrational excitation remains an open question. In this study, we address this issue by simulating the PIPT processes using a nonadiabatic molecular dynamics approach combined with real-time electron dynamics at the level of a semiempirical quantum chemical model, density-functional tight binding. The results show the importance of vibronic interactions in the PIPT processes, thereby suggesting the possibility of N → I PIPT by vibrational excitations with infrared irradiation.

Unveiling controlling factors of the S0/S1 minimum-energy conical intersection (3): Frozen orbital analysis based on the spin-flip theory.

Conical intersections (CIs), which indicate the crossing of two or more adiabatic electronic states, are crucial in the mechanisms of photophysical, photochemical, and photobiological processes. Although various geometries and energy levels have been reported using quantum chemical calculations, the systematic interpretation of the minimum energy CI (MECI) geometries is unclear. A previous study [Nakai et al., J. Phys. Chem. A 122, 8905 (2018)] performed frozen orbital analysis (FZOA) based on time-dependent density functional theory (TDDFT) at the MECI formed between the ground and first electronic excited states (S0/S1 MECI), thereby inductively clarifying two controlling factors. However, one of the factors that the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energy gap became close to the HOMO-LUMO Coulomb integral was not valid in the case of spin-flip TDDFT (SF-TDDFT), which is frequently used as a means of the geometry optimization of MECI [Inamori et al., J. Chem. Phys. 152, 144108 (2020)]. This study revisited the controlling factors using FZOA for the SF-TDDFT method. Based on spin-adopted configurations within a minimum active space, the S0-S1 excitation energy is approximately represented by the HOMO and LUMO energy gap ΔεHL, a contribution from Coulomb integrals JHL″ and that from the HOMO-LUMO exchange integral KHL″. Furthermore, numerical applications of the revised formula at the SF-TDDFT method confirmed the control factors of S0/S1 MECI.

Enabling large-scale quantum path integral molecular dynamics simulations through the integration of Dcdftbmd and i-PI codes.

A large-scale quantum chemical calculation program, Dcdftbmd, was integrated with a Python-based advanced atomistic simulation program, i-PI. The implementation of a client-server model enabled hierarchical parallelization with respect to replicas and force evaluations. The established framework demonstrated that quantum path integral molecular dynamics simulations can be executed with high efficiency for systems consisting of a few tens of replicas and containing thousands of atoms. The application of the framework to bulk water systems, with and without an excess proton, demonstrated that nuclear quantum effects are significant for intra- and inter-molecular structural properties, including oxygen-hydrogen bond distance and radial distribution function around the hydrated excess proton.

Neutrophil-to-lymphocyte ratio as an early marker of outcomes in patients with recurrent oral squamous cell carcinoma treated with nivolumab.

The immune checkpoint inhibitor (ICI), nivolumab, has revolutionised the treatment of recurrent and metastatic oral cancer. However, the response rate to ICIs remains low, and identifying predictors of nivolumab response is critical. Although the neutrophil-to-lymphocyte ratio (NLR) has been suggested as a predictive marker of nivolumab response in patients with various types of cancer, its utility in oral squamous cell carcinoma (OSCC) has not been elucidated. In this retrospective multicentre cohort study, we evaluated the association between NLR and outcome of nivolumab treatment in 64 patients with OSCC treated between 2017 and 2020. The objective response and disease control rates were 25.1% and 32.9%, respectively. The rates for complete and partial responses were 15.7% (10/64) and 9.4% (6/64), respectively; stable and progressive disease rates were 7.8% (5/64) and 67.1% (43/64), respectively. Complete and partial responses were classified as responders, and stable and progressive diseases were classified as non-responders. The median (range) pre-treatment NLR among responders was 4.3 (2.8-8.0), which decreased to 4.0 (2.6-6.3) after nivolumab treatment, and the median (range) pre-treatment NLR among non-responders was 5.1 (2.7-7.9), which increased to 6.4 (4.0-14.0) with tumour growth. Moreover, overall survival was significantly worse in the group with a higher post-treatment NLR (≥5) than in the group with a lower NLR (<5). Patients with a post-treatment NLR of ≥6 had worse outcomes for salvage chemotherapy following nivolumab treatment. Thus, post-treatment NLR could be a useful marker for predicting the response to nivolumab treatment or salvage chemotherapy in patients with OSCC.

Nanoscale and Real-Time Nuclear-Electronic Dynamics Simulation Study of Charge Transfer at the Donor-Acceptor Interface in Organic Photovoltaics.

Charge-transfer (CT) processes in donor-acceptor interfaces of organic photovoltaics have been challenging targets for computational chemistry owing to their nanoscale and ultrafast nature. Herein, we report real-time nuclear-electronic dynamics simulations of CT processes in a nanometer-scale donor-acceptor interface model composed of a donor poly(3-hexylthiophene-2,5-diyl) crystal and an acceptor [6,6]-phenyl-C61-butyric acid methyl ester aggregate. The simulations were realized using our original reduced-scaling computational technique, namely, patchwork-approximation-based Ehrenfest dynamics. The results illustrated the CT pathway with atomic resolution, thereby rationalizing the observed excitation-energy dependence of the quantity of CT. Further, nuclear motion, which is affected by the electronic dynamics, was observed to play a significant role in the CT process by modulating molecular orbital energies. The present study suggests that microscopic CT processes strongly depend on local structures of disordered donor-acceptor interfaces as well as coupling between nuclear and electronic dynamics.

Species-selective nanoreactor molecular dynamics simulations based on linear-scaling tight-binding quantum chemical calculations.

Here, extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events are presented. The species-selective algorithm, where the nanoreactor effectively works for the selected desired reactants, was introduced to the original scheme. Moreover, for efficient simulations of large model systems with the modified approach, the divide-and-conquer linear-scaling density functional tight-binding method was exploited. Two illustrative applications of the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions indicate that species-selective quantum chemical nanoreactor molecular dynamics is a promising method to accelerate the sampling of multicomponent chemical processes proceeding under relatively mild conditions.

Divide-and-Conquer Linear-Scaling Quantum Chemical Computations.

Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.

Experimental and Theoretical Evidence for Relativistic Catalytic Activity in C-H Activation of N-Phenylbenzamide Using a Cationic Iridium Complex.

This study elucidates that relativistic effect plays a key role in catalytic C-H activation using a cationic Ir complex. Experiments show that the cationic Ir(I)-diphosphine catalyst can be used for the deuterium substitution of N-phenylbenzamide, whereas a cationic Rh(I)-diphosphine catalyst is scarcely effective. Density functional theory calculations, including the relativistic effect, demonstrate a large difference in the reaction energy diagrams for the C-H activation of N-phenylbenzamide between the cationic Ir and Rh catalysts. In particular, the relatively low reaction barrier and considerably stabilized product obtained for the Ir catalysts are rationalized by strong Ir-C and Ir-H interactions, which originate from the relativistic self-consistent d-orbital expansion of Ir.

Quantum Algorithm of the Divide-and-Conquer Unitary Coupled Cluster Method with a Variational Quantum Eigensolver.

The variational quantum eigensolver (VQE) with shallow or constant-depth quantum circuits is one of the most pursued approaches in the noisy intermediate-scale quantum (NISQ) devices with incoherent errors. In this study, the divide-and-conquer (DC) linear scaling technique, which divides the entire system into several fragments, is applied to the VQE algorithm based on the unitary coupled cluster (UCC) method, denoted as DC-qUCC/VQE, to reduce the number of required qubits. The unitarity of the UCC ansatz that enables the evaluation of the total energy as well as various molecular properties as expectation values can be easily implemented on quantum devices because the quantum gates are unitary operators themselves. Based on this feature, the present DC-qUCC/VQE algorithm is designed to conserve the total number of electrons in the entire system using the density matrix evaluated on a quantum computer. Numerical assessments clarified that the energy errors of the DC-qUCC/VQE calculations decrease by using the constraint of the total number of electrons. Furthermore, the DC-qUCC/VQE algorithm could reduce the number of quantum gates and shows the possibility of decreasing incoherent errors.

Hydroxide Ion Mechanism for Long-Range Proton Pumping in the Third Proton Transfer of Bacteriorhodopsin.

In bacteriorhodopsin, representative light-driven proton pump, five proton transfers yield vectorial active proton translocation, resulting in a proton gradient in microbes. Third proton transfer occurs from Asp96 to the Schiff base on the photocycle, which is expected to be a long-range proton transfer via the Grotthuss mechanism through internal water molecules. Here, large-scale quantum molecular dynamics simulations are performed for the third proton transfer, where all the atoms (∼50000 atoms) are treated quantum-mechanically. The simulations demonstrate that two reaction paths exist along the water wire, namely, via hydronium and via hydroxide ions. The free energy analysis confirms that the path via hydroxide ions is considerably favorable and consistent with the observed lifetime of the transient water wire. Therefore, the proposed hydroxide ion mechanism, as in the first proton transfer, is responsible for the third long-range proton transfer.

Dynamic hetero-metallic bondings visualized by sequential atom imaging.

Traditionally, chemistry has been developed to obtain thermodynamically stable and isolable compounds such as molecules and solids by chemical reactions. However, recent developments in computational chemistry have placed increased importance on studying the dynamic assembly and disassembly of atoms and molecules formed in situ. This study directly visualizes the formation and dissociation dynamics of labile dimers and trimers at atomic resolution with elemental identification. The video recordings of many homo- and hetero-metallic dimers are carried out by combining scanning transmission electron microscopy (STEM) with elemental identification based on the Z-contrast principle. Even short-lived molecules with low probability of existence such as AuAg, AgCu, and AuAgCu are directly visualized as a result of identifying moving atoms at low electron doses.

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.

The main protease (Mpro) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) catalyzes the cleavage of polyproteins for viral replication. Here, large-scale quantum molecular dynamics and metadynamics simulations for ligand-free Mpro were performed, where all the atoms were treated quantum-mechanically, focusing on elucidation of the controversial active-site protonation state. The simulations clarified that the interconverting multiple protonation states exist in unliganded Mpro, and the catalytically relevant ion-pair state is more stable than the neutral state, which is consistent with neutron crystallography. The results highlight the importance of the ion-pair state for repurposing or discovering antiviral drugs that target Mpro.

Tetraaryldiborane(4) Can Emit Dual Fluorescence Responding to the Structural Change around the B-B Bond.

We report the successful synthesis of tetramesityldiborane(4) (Mes4 B2 ) through the reductive coupling of a dimesitylborinium ion. Owing to the steric protection conferred by the mesityl groups, Mes4 B2 shows exceptional chemical stability and remains intact in water. Single-crystal X-ray analysis revealed that Mes4 B2 has an orthogonal geometry, where the B-B center is completely hidden by the mesityl groups. Remarkably, Mes4 B2 emits dual fluorescence at 460 and 620 nm, both in solution and in the solid state. Theoretical calculations showed that Mes4 B2 in the excited S1 state adopts a twisted or planar geometry, which is responsible for the shorter- or longer-wavelength fluorescence, respectively. The intensity ratio of the dual fluorescence is sensitive to the viscosity of the medium, which suggests that Mes4 B2 has potential as a ratiometric viscosity sensor.

Direct Near Infrared Light-Activatable Phthalocyanine Catalysts.

The high penetration of near-infrared (NIR) light makes it effective for use in selective reactions under light-shielded conditions, such as in sealed reactors and deep tissues. Herein, we report the development of phthalocyanine catalysts directly activated by NIR light to transform small organic molecules. The desired photocatalytic properties were achieved in the phthalocyanines by introducing the appropriate peripheral substituents and central metal. These phthalocyanine photocatalysts promote cross-dehydrogenative-coupling (CDC) under irradiation with 810 nm NIR light. The choice of solvent is important, and a mixture of a reaction-accelerating (pyridine) and -decelerating (methanol) solvents was particularly effective. Moreover, we demonstrate photoreactions under visible-light-shielded conditions through the transmission of NIR light. A combined experimental and computational mechanistic analysis revealed that this NIR reaction does not involve a photoredox-type mechanism with electron transfer, but instead a singlet-oxygen-mediated mechanism with energy transfer.

Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian.

To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Numerical results for giant icosahedral fullerenes, which comprise up to 6000 atoms, suggest that the scaling of the present PA-based method is less than quadratic, which yields a significant advantage over the conventional cubic scaling method in terms of computational time. The acceleration by the parallelization on multiple nodes was also assessed. Furthermore, the electronic and structural dynamics resulting from the perturbation by the external electric field were accurately reproduced with the PA, even when the electronic excitation was spatially delocalized.