記述言語：英語   出版者・発行元：ACS Physical Chemistry Au  

Purple bacteria possess two ring-shaped protein complexes, light-harvesting 1 (LH1) and 2 (LH2), both of which function as antennas for solar energy utilization for photosynthesis but exhibit distinct absorption properties. The two antennas have differing amounts of bacteriochlorophyll (BChl) a; however, their significance in spectral tuning remains elusive. Here, we report a high-precision evaluation of the physicochemical factors contributing to the variation in absorption maxima between LH1 and LH2, namely, BChl a structural distortion, protein electrostatic interaction, excitonic coupling, and charge transfer (CT) effects, as derived from detailed spectral calculations using an extended version of the exciton model, in the model purple bacterium Rhodospirillum rubrum. Spectral analysis confirmed that the electronic structure of the excited state in LH1 extended to the BChl a 16-mer. Further analysis revealed that the LH1-specific redshift (∼61% in energy) is predominantly accounted for by the CT effect resulting from the closer inter-BChl distance in LH1 than in LH2. Our analysis explains how LH1 and LH2, both with chemically identical BChl a chromophores, use distinct physicochemical effects to achieve a progressive redshift from LH2 to LH1, ensuring efficient energy transfer to the reaction center special pair.

DOI： 10.1021/acsphyschemau.4c00022

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記述言語：英語   出版者・発行元：Journal of the American Chemical Society  

Sulfur-bridged cationic diazulenomethenes were synthesized and exhibited high stability even under basic conditions due to the delocalization of positive charge over the whole π-conjugated skeleton. As a result of the effective delocalization and the absence of orthogonally oriented bulky substituents, the cationic π-conjugated skeletons formed a π-stacked array with short interfacial distances. A derivative with SbF6- as a counter anion formed a charge-segregated assembly in the crystalline state, rather than the generally favored charge-by-charge arrangement of oppositely charged species based on electrostatic interactions. Theoretical calculations suggested that the destabilization caused by electrostatic repulsion between two positively charged π-conjugated skeletons is compensated by the dispersion forces. In addition, the counter anion SbF6- played a role in regulating the molecular alignment through F⋯H-C and F-S interactions, which resulted in the charge-segregated alignment of the cationic π-skeletons. This characteristic assembled structure gave rise to a high charge-carrier mobility of 1.7 cm2 V-1 s-1 as determined using flash-photolysis time-resolved microwave conductivity.

DOI： 10.1021/jacs.4c07122

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記述言語：英語   出版者・発行元：Angewandte Chemie - International Edition  

Embedding two boron atoms into a polycyclic aromatic hydrocarbon (PAH) leads to the formation of a neutral analogue that is isoelectronic to the corresponding dicationic PAH skeleton, which can significantly alter its electronic structure. Based on this concept, we explore herein the identification of near-infrared (NIR)-emissive PAHs with the aid of an in silico screening method. Using perylene as the PAH scaffold, we embedded two boron atoms and fused two thiophene rings to it. Based on this design concept, all possible structures (ca. 2500 entities) were generated using a comprehensive structure generator. Time-dependent DFT calculations were conducted on all these structures, and promising candidates were extracted based on the vertical excitation energy, transition dipole moment, and atomization energy per bond. One of the extracted dithieno-diboraperylene candidates was synthesized and indeed exhibited emission at 724 nm with a quantum yield of 0.40 in toluene, demonstrating the validity of this screening method. This modification was further applied to other PAHs, and a series of thienobora-modified PAHs was synthesized.

DOI： 10.1002/anie.202403829

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記述言語：英語   出版者・発行元：Journal of Physical Chemistry Letters  

Channelrhodopsin (ChR) and heliorhodopsin (HeR) are microbial rhodopsins with similar structures but different circular dichroism (CD) spectra: ChR shows biphasic negative and positive bands, whereas HeR shows a single positive band. We explored the physicochemical factors underlying these differences through computational methods. Using the exciton model based on first-principles computations, we obtained the CD spectra of ChR and HeR. The obtained spectra indicate that the protein dimer structures and the quantum mechanical treatment of the retinal chromophore and its interacting amino acids are crucial for accurately reproducing the experimental spectra. Further calculations revealed that the sign of the excitonic coupling was opposite between the ChR and HeR dimers, which was attributed to the contrasting second term of the orientation factor between the two retinal chromophores. These findings demonstrate that slight variations in the intermolecular orientation of the two chromophores can result in significant differences in the CD spectral shape.

DOI： 10.1021/acs.jpclett.4c00879

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記述言語：英語   出版者・発行元：Journal of Chemical Physics  

Chemical phenomena involving near-degenerate electronic states, such as conical intersections or avoided crossing, can be properly described using quasi-degenerate perturbation theory. This study proposed a highly scalable quasi-degenerate second-order N-electron valence state perturbation theory (QD-NEVPT2) using the local pair-natural orbital (PNO) method. Our recent study showed an efficient implementation of the PNO-based state-specific NEVPT2 method using orthonormal localized virtual molecular orbitals (LVMOs) as an intermediate local basis. This study derived the state-coupling (or off-diagonal) terms to implement QD-NEVPT2 in an alternative manner to enhance efficiency based on the internally contracted basis and PNO overlap matrices between different references. To facilitate further acceleration, a local resolution-of-the-identity (RI) three-index integral generation algorithm was developed using LMOs and LVMOs. Although the NEVPT2 theory is considered to be less susceptible to the intruder-state problem (ISP), this study revealed that it can easily suffer from ISP when calculating high-lying excited states. We ameliorated this instability using the imaginary level shift technique. The PNO-QD-NEVPT2 calculations were performed on small organic molecules for the 30 lowest-lying states, as well as photoisomerization involving the conical intersection of 1,1-dimethyldibenzo[b,f] silepin with a cis-stilbene skeleton. These calculations revealed that the PNO-QD-NEVPT2 method yielded negligible errors compared to the canonical QD-NEVPT2 results. Furthermore, we tested its applicability to a large photoisomerization system using the green fluorescent protein model and the ten-state calculation of the large transition metal complex, showcasing that off-diagonal elements can be evaluated at a relatively low cost.

DOI： 10.1063/5.0204419

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記述言語：英語   出版者・発行元：Science Advances  

Thermally activated delayed fluorescence (TADF) materials and multi-resonant (MR) variants are promising organic emitters that can achieve an internal electroluminescence quantum efficiency of ~100%. The reverse intersystem crossing (RISC) is key for harnessing triplet energies for fluorescence. Theoretical modeling is thus crucial to estimate its rate constant (kRISC) for material development. Here, we present a comprehensive assessment of the theory for simulating the RISC of MR-TADF molecules within a perturbative excited-state dynamics framework. Our extended rate formula reveals the importance of the concerted effects of nonadiabatic spin-vibronic coupling and vibrationally induced spin-orbital couplings in reliably determining kRISC of MR-TADF molecules. The excited singlet-triplet energy gap is another factor influencing kRISC. We present a scheme for gap estimation using experimental Arrhenius plots of kRISC. Erroneous behavior caused by approximations in Marcus theory is elucidated by testing 121 MR-TADF molecules. Our extended modeling offers in-depth descriptions of kRISC

DOI： 10.1126/sciadv.adk3219

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記述言語：英語   出版者・発行元：Journal of the American Chemical Society  

The light-harvesting antennae of diatoms and spinach are composed of similar chromophores; however, they exhibit different absorption wavelengths. Recent advances in cryoelectron microscopy have revealed that the diatom light-harvesting antenna fucoxanthin chlorophyll a/c-binding protein (FCPII) forms a tetramer and differs from the spinach antenna in terms of the number of protomers; however, the detailed molecular mechanism remains elusive. Herein, we report the physicochemical factors contributing to the characteristic light absorption of the diatom light-harvesting antenna based on spectral calculations using an exciton model. Spectral analysis reveals the significant contribution of unique fucoxanthin molecules (fucoxanthin-S) in FCPII to the diatom-specific spectrum, and further analysis determines their essential role in excitation-energy transfer to chlorophyll. It was revealed that the specificity of these fucoxanthin-S molecules is caused by the proximity between protomers associated with the tetramerization of FCPII. The findings of this study demonstrate that diatoms employ fucoxanthin-S to harvest energy under the ocean in the absence of long-wavelength sunlight and can provide significant information about the survival strategies of photosynthetic organisms to adjust to their living environment.

DOI： 10.1021/jacs.3c12045

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記述言語：英語   出版者・発行元：ACS Physical Chemistry Au  

Incorporation of the phosphorus element into a π-conjugated skeleton offers valuable prospects for adjusting the electronic structure of the resulting functional π-electron systems. Trivalent phosphorus has the potential to decrease the LUMO level through σ*−π* interaction, which is further enhanced by its oxygenation to the pentavalent P center. This study shows that utilizing our computational analysis to examine excited-state dynamics based on radiative/nonradiative rate constants and fluorescence quantum yield (ΦF) is effective for analyzing the photophysical properties of P-containing organic dyes. We theoretically investigate how the trivalent phosphanyl group and pentavalent phosphine oxide moieties affect radiative and nonradiative decay processes. We evaluate four variations of P-bridged stilbene analogs. Our analysis reveals that the primary decay pathway for photoexcited bis-phosphanyl-bridged stilbene is the intersystem crossing (ISC) to the triplet state and nonradiative. The oxidation of the phosphine moiety, however, suppresses the ISC due to the relative destabilization of the triplet states. The calculated rate constants match an increase in experimental ΦF from 0.07 to 0.98, as simulated from 0.23 to 0.94. The reduced HOMO-LUMO gap supports a red shift in the fluorescence spectra relative to the phosphine analog. The thiophene-fused variant with the nonoxidized trivalent P center exhibits intense emission with a high ΦF, 0.95. Our prediction indicates that the ISC transfer is obstructed owing to the relatively destabilized triplet state induced by the thiophene substitution. Conversely, the thiophene-fused analog with the phosphine oxide moieties triggers a high-rate internal conversion mediated by conical intersection, leading to a decreased ΦF

DOI： 10.1021/acsphyschemau.3c00038

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Physical Chemistry Chemical Physics  

Nafamostat and camostat are known to inhibit the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by forming a covalent bond with the human transmembrane serine protease 2 (TMPRSS2) enzyme. Previous experiments revealed that the TMPRSS2 inhibitory activity of nafamostat surpasses that of camostat, despite their structural similarities; however, the molecular mechanism of TMPRSS2 inhibition remains elusive. Herein, we report the energy profiles of the acylation reactions of nafamostat, camostat, and a nafamostat derivative by quantum chemical calculations using a combined molecular cluster and polarizable continuum model (PCM) approach. We further discuss the physicochemical relevance of their inhibitory activity in terms of thermodynamics and kinetics. Our analysis attributes the strong inhibitory activity of nafamostat to the formation of a stable acyl intermediate and its low activation energy during acylation with TMPRSS2. The proposed approach is also promising for elucidating the molecular mechanisms of other covalent drugs.

DOI： 10.1039/d3cp01723k

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掲載種別：研究論文（学術雑誌）   出版者・発行元：Digital Discovery  

Artificial neural networks (ANNs) for material modeling have received significant interest. We recently reported an adaptation of ANNs based on Boltzmann machine (BM) architectures to an ansatz of the multiconfigurational many-electron wavefunction, denoted as a neural-network quantum state (NQS), for quantum chemistry calculations [Yang et al., J. Chem. Theory Comput., 2020, 16, 3513–3529]. Here, this study presents its extended formalism to a quantum algorithm that enables the preparation of the NQS through quantum gates. The descriptors of the ANN model, which are chosen as the occupancies of electronic configurations, are quantum-mechanically represented by qubits. Our algorithm may thus bring potential advantages over classical sampling-based computation employed in previous studies. The NQS can be accurately formed using quantum-native procedures. Still, the training of the model in terms of energy minimization is efficiently performed on a classical computer; thus, our approach is a class of variational quantum eigensolvers. The BM models are related to the Gibbs distribution, and our preparation procedures exploit techniques of quantum phase estimation but with no Hamiltonian evolution. The proposed algorithm is assessed by implementing it on a quantum computer simulator. Illustrative molecular calculations at the complete-active-space configuration interaction level of theory are displayed, confirming consistency with the accuracy of our previous classical approaches.

DOI： 10.1039/d2dd00093h

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

Second-order N-electron valence state perturbation theory (NEVPT2) is an exactly size-consistent and intruder-state-free multi-reference theory. To accelerate the NEVPT2 computation, Guo and Neese combined it with the local pair-natural orbital (PNO) method using the projected atomic orbitals (PAOs) as the underlying local basis [Guo et al., J. Chem. Phys. 144, 094111 (2016)]. In this paper, we report the further development of the PNO-NEVPT2 method using the orthonormal and non-redundant localized virtual molecular orbitals (LVMOs) instead of PAOs. The LVMOs were previously considered to perform relatively poor compared to PAOs because the resulting orbital domains were unacceptably large. Our prior work, however, showed that this drawback can be remedied by re-forming the domain construction scheme using differential overlap integrals [Saitow et al., J. Chem. Phys. 157, 084101 (2022)]. In this work, we develop further refinements to enhance the feasibility of using LVMOs. We first developed a two-level semi-local approach for screening out so-called weak-pairs to select or truncate the pairs for PNO constructions more flexibly. As a refinement specific to the Pipek-Mezey localization for LVMOs, we introduced an iterative scheme to truncate the Givens rotations using varying thresholds. We assessed the LVMO-based PNO-NEVPT2 method through benchmark calculations for linear phenyl alkanes, which demonstrate that it performs comparably well relative to the PAO-based approach. In addition, we evaluated the Co-C bond dissociation energies for the cobalamin derivatives composed of 200 or more atoms, which confirms that the LVMO-based method can recover more than 99.85% of the canonical NEVPT2 correlation energy.

DOI： 10.1063/5.0143793

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Angewandte Chemie - International Edition  

Catalytic systems using a small amount of organic photosensitizer for the activation of an inorganic (on-demand ligand-free) nickel(II) salt represent a cost-effective method for cross-coupling reactions, while C(sp2)−O bond formation remains less developed. Herein, we report a strategy for the synthesis of phenols with a nickel(II) salt and an organic photosensitizer, which was identified via an investigation into the catalytic activity of 60 organic photosensitizers consisting of various electron donor and acceptor moieties. To examine the effect of multiple intractable parameters on the catalytic activity of photosensitizers, machine-learning (ML) models were developed, wherein we embedded descriptors representing their physical and structural properties, which were obtained from DFT calculations and RDKit, respectively. The study clarified that integrating both DFT- and RDKit-derived descriptors in ML models balances higher “precision” and “recall” across a wide range of search space relative to using only one of the two descriptor sets.

DOI： 10.1002/anie.202219107

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202219107

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry Letters  

The visual pigments of the cones perceive red, green, and blue colors. The monkey green (MG) pigment possesses a unique Cl- binding site; however, its relationship to the spectral tuning in green pigments remains elusive. Recently, FTIR spectroscopy revealed the characteristic structural modifications of the retinal binding site by Cl- binding. Herein, we report the computational structural modeling of MG pigments and quantum-chemical simulation to investigate its spectral redshift and physicochemical relevance when Cl- is present. Our protein structures reflect the previously suggested structural changes. AlphaFold2 failed to predict these structural changes. Excited-state calculations successfully reproduced the experimental red-shifted absorption energies, corroborating our protein structures. Electrostatic energy decomposition revealed that the redshift results from the His197 protonation state and conformations of Glu129, Ser202, and Ala308; however, Cl- itself contributes to the blueshift. Site-directed mutagenesis supported our analysis. These modeled structures may provide a valuable foundation for studying cone pigments.

DOI： 10.1021/acs.jpclett.2c03619

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

We present an algorithm for evaluating analytic nuclear energy gradients of the state-averaged density matrix renormalization group complete-active-space self-consistent field (SA-DMRG-CASSCF) theory based on the newly derived coupled-perturbed (CP) DMRG-CASSCF equations. The Lagrangian for the conventional SA-CASSCF analytic gradient theory is extended to the SA-DMRG-CASSCF variant that can fully consider a whole set of constraints on the parameters of multi-root canonical matrix product states formed at all the DMRG block configurations. An efficient algorithm to solve the CP-DMRG-CASSCF equations for determining the multipliers was developed. The complexity of the resultant analytic gradient algorithm is overall the same as that of the unperturbed SA-DMRG-CASSCF algorithm. In addition, a reduced-scaling approach was developed to directly compute the SA reduced density matrices (SA-RDMs) and their perturbed ones without calculating separate state-specific RDMs. As part of our implementation scheme, we neglect the term associated with the constraint on the active orbitals in terms of the active-active rotation in the Lagrangian. Thus, errors from the true analytic gradients may be caused in this scheme. The proposed gradient algorithm was tested with the spin-adapted implementation by checking how accurately the computed analytic energy gradients reproduce numerical gradients of the SA-DMRG-CASSCF energies using a common number of renormalized bases. The illustrative applications show that the errors are sufficiently small when using a typical number of the renormalized bases, which is required to attain adequate accuracy in DMRG's total energies.

DOI： 10.1063/5.0130636

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

DOI： 10.1063/5.0135257

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ACS Chemical Biology  

Stomata are pores in the leaf epidermis of plants and their opening and closing regulate gas exchange and water transpiration. Stomatal movements play key roles in both plant growth and stress responses. In recent years, small molecules regulating stomatal movements have been used as a powerful tool in mechanistic studies, as well as key players for agricultural applications. Therefore, the development of new molecules regulating stomatal movement and the elucidation of their mechanisms have attracted much attention. We herein describe the discovery of 2,6-dihalopurines, AUs, as a new stomatal opening inhibitor, and their mechanistic study. Based on biological assays, AUs may involve in the pathway related with plasma membrane H+-ATPase phosphorylation. In addition, we identified leucine-rich repeat extensin proteins (LRXs), LRX3, LRX4 and LRX5 as well as RALF, as target protein candidates of AUs by affinity based pull down assay and molecular dynamics simulation. The mechanism of stomatal movement related with the LRXs-RALF is an unexplored pathway, and therefore further studies may lead to the discovery of new signaling pathways and regulatory factors in the stomatal movement.

DOI： 10.1021/acschembio.2c00771

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of the American Chemical Society  

We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.

DOI： 10.1021/jacs.2c07299

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Plant and Cell Physiology  

The circadian clock, an internal time-keeping system with a period of about 24 h, coordinates many physiological processes with the day-night cycle. We previously demonstrated that BML-259 [N-(5-isopropyl-2-thiazolyl) phenylacetamide], a small molecule with mammal CYCLIN DEPENDENT KINASE 5 (CDK5)/CDK2 inhibition activity, lengthens Arabidopsis thaliana (Arabidopsis) circadian clock periods. BML-259 inhibits Arabidopsis CDKC kinase, which phosphorylates RNA polymerase II in the general transcriptional machinery. To accelerate our understanding of the inhibitory mechanism of BML-259 on CDKC, we performed structure-function studies of BML-259 using circadian period-lengthening activity as an estimation of CDKC inhibitor activity in vivo. The presence of a thiazole ring is essential for period-lengthening activity, whereas acetamide, isopropyl and phenyl groups can be modified without effect. BML-259 analog TT-539, a known mammal CDK5 inhibitor, did not lengthen the period nor did it inhibit Pol II phosphorylation. TT-361, an analog having a thiophenyl ring instead of a phenyl ring, possesses stronger period-lengthening activity and CDKC;2 inhibitory activity than BML-259. In silico ensemble docking calculations using Arabidopsis CDKC;2 obtained by a homology modeling indicated that the different binding conformations between these molecules and CDKC;2 explain the divergent activities of TT539 and TT361.

DOI： 10.1093/pcp/pcac127

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その他リンク： https://academic.oup.com/pcp/article-pdf/63/11/1720/47195497/pcac127.pdf

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Cell Reports Physical Science  

A bowl-shaped π-conjugated molecule typically undergoes bowl-inversion motion via a planarized transition state (TS), the highest-energy state along the reaction coordinate between two minimum bowl structures. Isolation of such planarized state has been challenging. Here, we report that a platinum(II) complex of antiaromatic porphyrin, norcorrole, adopts bowl-shaped conformation in solution but can become planar in solid. In the crystalline state, the norcorrole Pt(II) complex forms triple-decker stacking structures, in which the planarized norcorrole is stabilized and sandwiched between two bowl-shaped norcorroles. The planar conformation corresponds to the TS structure in the dynamic bowl-to-bowl inversion motion of the bowl-shaped molecule. Detailed theoretical studies have revealed that the intrinsically unstable planar conformation is stabilized by the dispersion force among the substituents and enhanced Pt–Pt interactions created by the antiaromatic macrocyclic ligand.

DOI： 10.1016/j.xcrp.2022.101045

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Scientific Reports  

The orientation factor of fluorescence resonance energy transfer (FRET) between photosynthetic light-harvesting 2 complex (LH2) and artificial fluorophore (Alexa Fluor 647: A647) was theoretically investigated. The orientation factor of 2/3, i.e., the isotropic mean, is widely used to predict the donor–acceptor distance from FRET measurements. However, this approximation seems inappropriate because the movement of A647 is possibly restricted by the bifunctional linker binding to LH2. In this study, we performed molecular dynamics (MD) simulations and electronic coupling calculations on the LH2-A647 conjugate to analyze its orientation factor. The MD results showed that A647 keeps a position approximately 26 Å away from the bacteriochlorophyll (BChl) assembly in LH2. The effective orientation factor was extracted from the electronic coupling calculated using the transition charge from electrostatic potential (TrESP) method. With MD snapshots, an averaged orientation factor was predicted to be 1.55, significantly different from the isotropic mean value. The analysis also suggested that the value of the refractive index employed in the previous studies is not suitable for this system. Furthermore, optimal orientations of A647 with larger orientation factors to improve FRET efficiency were searched using Euler angles. The present approach is useful for extending the applicability of FRET analysis.

DOI： 10.1038/s41598-022-19375-2

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その他リンク： https://www.nature.com/articles/s41598-022-19375-2

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

The multireference second-order perturbation theory (CASPT2) is known to deliver a quantitative description of various complex electronic states. Despite its near-size-consistent nature, the applicability of the CASPT2 method to large, real-life systems is mostly hindered by large computational and storage costs for the two-external tensors, such as two-electron integrals, amplitudes, and residuum. To this end, Menezes and co-workers developed a reduced-scaling CASPT2 scheme by incorporating the local pair-natural orbital (PNO) representation of the many-body wave functions using non-orthonormal projected atomic orbitals (PAOs) into the CASPT theory [F. Menezes et al., J. Chem. Phys. 145, 124115 (2016)]. Alternatively, in this paper, we develop a new PNO-based CASPT2 scheme using the orthonormal localized virtual molecular orbitals (LVMOs) and assess its performance and accuracy in comparison with the conventional PAO-based counterpart. Albeit the compactness, the LVMOs were considered to perform somewhat poorly compared to PAOs in the local correlation framework because they caused enormously large orbital domains. In this work, we show that the size of LVMO domains can be rendered comparable to or even smaller than that of PAOs by the use of the differential overlap integrals for domain construction. Optimality of the MOs from the CASSCF treatment is a key to reducing the LVMO domain size for the multireference case. Due to the augmented Hessian-based localization algorithm, an additional computational cost for obtaining the LVMOs is relatively minor. We demonstrate that the LVMO-based PNO-CASPT2 method is routinely applicable to large, real-life molecules such as Menshutkin SN2 reaction in a single-walled carbon nanotube reaction field.

DOI： 10.1063/5.0094777

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掲載種別：研究論文（学術雑誌）   出版者・発行元：ACS Catalysis  

The desulfonylative radical addition of tertiary alkyl groups to gem-difluoroalkenes by photoredox Ir-catalyst is described. This method exhibits broad substrate scope, affording structurally diverse (E)-fluoroalkene derivatives in a highly stereoselective manner. The resulting (E)-fluoroalkenes were converted into complex fused cyclic compounds by intramolecular cyclization reactions. Control experiments and theoretical calculations are consistent with a single Ir catalyst playing the dual role of generating radical species from sulfones via single electron transfer and mediating Z/E isomerization via energy transfer. A subset of fluoroalkenes provided Z stereoisomers with >90% selectivity, but the same alkenes could also be obtained as E isomers with high selectivity by taking advantage of a secondary Z to E photoisomerization.

DOI： 10.1021/acscatal.2c02233

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Angewandte Chemie - International Edition  

We report on the fluorescence properties of a new class of emissive and stable π-radicals that contain a boron atom at a position distant from the radical center. A fully planarized derivative exhibited an intense red fluorescence with high fluorescence quantum yields (ΦF >0.67) even in polar solvents. To elucidate the origin of this phenomenon, we synthesized another boron-stabilized radical that contains a bulky aryl group on the boron atom. A comparison of these derivatives, as well as with conventional donor–π–acceptor (D–π–A)-type emissive π-radicals, unveiled several characteristic features in their photophysical properties. A theoretical analysis revealed that the SOMO–LUMO electronic transition generates an emissive D1 state. Unlike conventional D–π–A-type π-radicals, this state does not undergo significant structural relaxation. The boron-stabilized π-radicals demonstrated promising potential for organic light-emitting diodes as an emitting material.

DOI： 10.1002/anie.202201965

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202201965

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

A second-order many-body perturbation correction to the relativistic Dirac-Hartree-Fock energy is evaluated stochastically by integrating 13-dimensional products of four-component spinors and Coulomb potentials. The integration in the real space of electron coordinates is carried out by the Monte Carlo (MC) method with the Metropolis sampling, whereas the MC integration in the imaginary-time domain is performed by the inverse-cumulative distribution function method. The computational cost to reach a given relative statistical error for spatially compact but heavy molecules is observed to be no worse than cubic and possibly quadratic with the number of electrons or basis functions. This is a vast improvement over the quintic scaling of the conventional, deterministic second-order many-body perturbation method. The algorithm is also easily and efficiently parallelized with 92% strong scalability going from 64 to 4096 processors.

DOI： 10.1063/5.0091973

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その他リンク： https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0091973/16543411/224102_1_online.pdf

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ACS Omega  

We propose a novel machine-learning-based scoring function for drug discovery that incorporates ligand and protein structural information into a knowledge-based PMF score. Molecular docking, a simulation method for structure-based drug design (SBDD), is expected to reduce the enormous costs associated with conventional experimental methods in terms of rational drug discovery. Molecular docking has two main purposes: to predict ligand-binding structures for target proteins and to predict protein-ligand binding affinity. Currently available programs of molecular docking offer an accurate prediction of ligand binding structures for many systems. However, the accurate prediction of binding affinity remains challenging. In this study, we developed a new scoring function that incorporates fingerprints representing ligand and protein structures as descriptors in the PMF score. Here, regression analysis of the scoring function was performed using the following machine learning techniques: least absolute shrinkage and selection operator (LASSO) and light gradient boosting machine (LightGBM). The results on a test data set showed that the binding affinity delivered by the newly developed scoring function has a Pearson correlation coefficient of 0.79 with the experimental value, which surpasses that of the conventional scoring functions. Further analysis provided a chemical understanding of the descriptors that contributed significantly to the improvement in prediction accuracy. Our approach and findings are useful for rational drug discovery.

DOI： 10.1021/acsomega.2c02822

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Chemical Communications  

We synthesised thionium-ion embedded aromatic porphyrinoids: a free-base 5-thiaporphyrinium cation and its zinc complex. The sulphur atom effectively participates in the macrocyclic π-conjugation. Fluorescence quantum yields of thiaporphyrinium cations were lower than 1% unlike oxaporphyrinium cations. Detailed photophysical analysis and DFT calculations clarified the vibrational mode regarding the out-of-plane motion of the sulphur atom induced ultrafast quenching of the excited state in comparison to the corresponding oxaporphyrinium cations.

DOI： 10.1039/d2cc00522k

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of the American Chemical Society  

A periodic monolayer array of discrete C60s was generated on an atomically flat Au(111) surface with the aid of a template adlayer. The template was a two-dimensional (2D) array of molecular pits prepared on an Au(111) surface through 2D crystallization of shape-persistent macrocycles composed of four carbazole and four salphens/Ni-salphens with a 1 nm hollow. Scanning tunneling microscopy imaging under ultra-high vacuum revealed that the square-shaped macrocycles, with 1.5 nm sides, were arranged with a periodic spacing of approximately 4.0 nm on the Au(111) surface, where the orientation and periodicity of the macrocycles were dependent on their chemical structures. After sublimation of C60s onto the adlayer, a single C60 molecule was entrapped in each pit, and an ordered molecular array of C60s was attained with a pattern similar to that of the macrocycles. The periodic pattern of C60s on the surface was thermally stable up to approximately 200 °C, even under ambient pressure. Scanning tunneling spectroscopy suggested the existence of an electronic interaction between the C60s and the Au(111) surface that was influenced by the macrocycle template on the surface.

DOI： 10.1021/jacs.1c13610

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Plant and Cell Physiology  

The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.

DOI： 10.1093/pcp/pcac011

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その他リンク： https://academic.oup.com/pcp/article-pdf/63/4/450/43396790/pcac011.pdf

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry A  

Cinnamate derivatives show a variety of photo-induced reactions. Among them is trans-cis photoisomerization, which may involve the nonradiative decay (NRD) process. The extended multistate complete active space second-order perturbation (XMS-CASPT2) method was used in this study as a suitable theory for treating multireference electronic nature, which was frequently manifested in the photoisomerization process. The minimum energy paths of the trans-cis photoisomerization process of cinnamate derivatives were determined, and the activation energies were estimated using the resulting intrinsic reaction coordinate (IRC) paths. Natural orbital analysis revealed that the transition state's (TS) electronic structure is zwitterionic-like, elucidating the solvent and substituent effect on the energy barrier of photoisomerization paths. Furthermore, it was found that the charge on the pyramidalized carbon atom at the TS structure was strongly correlated with the activation energy barrier for the cinnamate derivatives. Thus, it seemingly provided a physical picture of the photoisomerization of cinnamates and was a good descriptor potentially applicable to molecular design for controlling the rate constant of the photoisomerization reaction.

DOI： 10.1021/acs.jpca.1c08504

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Viruses  

Inhibition of transmembrane serine protease 2 (TMPRSS2) is expected to block the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nafamostat, a potent TMPRSS2 inhibitor as well as a candidate for anti-SARS-CoV-2 drug, possesses the same acyl substructure as camostat, but is known to have a greater antiviral effect. A unique aspect of the molecular binding of nafamostat has been recently reported to be the formation of a covalent bond between its acyl substructure and Ser441 in TMPRSS2. In this study, we investigated crucial elements that cause the difference in anti-SARS-CoV-2 activity of nafamostat and camostat. In silico analysis showed that Asp435 significantly contributes to the binding of nafamostat and camostat to TMPRSS2, while Glu299 interacts strongly only with nafamostat. The estimated binding affinity for each compound with TMPRSS2 was actually consistent with the higher activity of nafamostat; however, the evaluation of the newly synthesized nafamostat derivatives revealed that the predicted binding affinity did not correlate with their anti-SARS-CoV-2 activity measured by the cytopathic effect (CPE) inhibition assay. It was further shown that the substitution of the ester bond with amide bond in nafamostat resulted in significantly weakened anti-SARS-CoV-2 activity. These results strongly indicate that the ease of covalent bond formation with Ser441 in TMPRSS2 possibly plays a major role in the anti-SARS-CoV-2 effect of nafamostat and its derivatives.

DOI： 10.3390/v14020389

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：JACS Au  

Hybrid density functional theory (B3LYP) and density matrix renormalization group (DMRG) theory have been used to quantitatively compare the degree of ligand noninnocence (corrole radical character) in seven archetypal metallocorroles. The seven complexes, in decreasing order of corrole noninnocent character, are Mn[Cor]Cl > Fe[Cor]Cl > Fe[Cor](NO) > Mo[Cor]Cl2 > Ru[Cor](NO) ≈ Mn[Cor]Ph ≈ Fe[Cor]Ph ≈ 0, where [Cor] refers to the unsubstituted corrolato ligand. DMRG-based second-order perturbation theory calculations have also yielded detailed excited-state energetics data on the compounds, shedding light on periodic trends involving middle transition elements. Thus, whereas the ground state of Fe[Cor](NO) (S = 0) is best described as a locally S = 1/2 {FeNO}7 unit antiferromagnetically coupled to a corrole A′ radical, the calculations confirm that Ru[Cor](NO) may be described as simply {RuNO}6-Cor3-, that is, having an innocent corrole macrocycle. Furthermore, whereas the ferromagnetically coupled S = 1{FeNO}7-Cor•2- state of Fe[Cor](NO) is only ∼17.5 kcal/mol higher than the S = 0 ground state, the analogous triplet state of Ru[Cor](NO) is higher by a far larger margin (37.4 kcal/mol) relative to the ground state. In the same vein, Mo[Cor]Cl2 exhibits an adiabatic doublet-quartet gap of 36.1 kcal/mol. The large energy gaps associated with metal-ligand spin coupling in Ru[Cor](NO) and Mo[Cor]Cl2 reflect the much greater covalent character of 4d-πinteractions relative to analogous interactions involving 3d orbitals. As far as excited-state energetics is concerned, DMRG-CASPT2 calculations provide moderate validation for hybrid density functional theory (B3LYP) for qualitative purposes, but underscore the possibility of large errors (>10 kcal/mol) in interstate energy differences.

DOI： 10.1021/jacsau.1c00417

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry A  

The polarizable continuum model (PCM) has been one of the most widely used approaches to take into account the solvation effect in quantum chemical calculations. In this paper, we performed a series of benchmark calculations to assess the accuracy of the PCM scheme combined with the second-order complete-active-space perturbation theory (CASPT2) for molecular systems in polar solvents. For solute molecules with extensive conjugated π orbitals, exemplified by elongated conjugated arylcarbenes, we have incorporated the ab initio density matrix renormalization group algorithm into the PCM-CASPT2 method. In the previous work, we presented a combination of the DMRG-CASPT2 method with the reference interaction site model (RISM) theory for describing the solvation effect using the radial distribution function and compared its performance to the widely used density-functional approaches (PCM-TD-DFT). The work here allows us to further show a more thorough assessment of the RISM model compared to the PCM with an equal level of the wave function treatment, the (DMRG-)CASPT2 theory, toward a high-accuracy electronic structure calculations for solvated chemical systems. With the exception that the PCM models are not capable of properly describing the hydrogen bondings, accuracy of the PCM-CASPT2 model is in most cases quite comparable to the RISM counterpart. (Figure Presented)

DOI： 10.1021/acs.jpca.1c05944

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry B  

Excited states of two kinds of bacteriochlorophyll (BChl) aggregates, B850 and B800, in photosynthetic light-harvesting complex II (LH2) are theoretically investigated by developing and using an extended exciton model considering efficiently evaluated excitonic coupling. Our exciton model based on dimer fragmentation is shown to reproduce the experimental absorption spectrum of LH2 with good accuracy, entailing their different redshifts originating from aggregations of B850 and B800. The systematic analysis has been performed on the spectra by quantitatively decomposing their spectral shift energies into the contributions of various effects: structural distortion, electrostatic, excitonic coupling, and charge-transfer (CT) effects. Our results show that the spectral redshift of B800 is mainly attributed to its electrostatic interaction with the protein environment, while that of B850 arises from the marked effect of the excitonic coupling between BChl units. The interchromophore CT excitation also plays a key role in the spectral redshift of B850. This CT effect can be effectively described using our dimer model. This suited characterization reveals that the pronounced CT effect originates from the characteristics of B850 that has closely spaced BChls as dimers. We highlight the importance of the refinement of the crystal structure with the use of quantum chemical methods for prediction of the spectrum.

DOI： 10.1021/acs.jpcb.1c04457

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Chemical Science  

The use of donor-π-acceptor (D-π-A) skeletons is an effective strategy for the design of fluorophores with red-shifted emission. In particular, the use of amino and boryl moieties as the electron-donating and -accepting groups, respectively, can produce dyes that exhibit high fluorescence and solvatochromism. Herein, we introduce a dithienophosphole P-oxide scaffold as an acceptor-spacer to produce a boryl- and amino-substituted donor-acceptor-acceptor (D-A-A) π-system. The thus obtained fluorophores exhibit emission in the near-infrared (NIR) region, while maintaining high fluorescence quantum yields even in polar solvents (e.g. λem = 704 nm and ΦF = 0.69 in CH3CN). A comparison of these compounds with their formyl- or cyano-substituted counterparts demonstrated the importance of the boryl group for generating intense emission. The differences among these electron-accepting substituents were examined in detail using theoretical calculations, which revealed the crucial role of the boryl group in lowering the nonradiative decay rate constant by decreasing the non-adiabatic coupling in the internal conversion process. The D-A-A framework was further fine-tuned to improve the photostability. One of these D-A-A dyes was successfully used in bioimaging to visualize the blood vessels of Japanese medaka larvae and mouse brain.

DOI： 10.1039/d1sc00827g

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry A  

The alkaline earth metal trimer cluster dianions Be32- and Mg32- lie energetically above their respective monoanions and can therefore decay by electron autodetachment. Consequently, these dianions possess only short-lived resonance states, and here we study these states using regularized analytic continuation as well as complex absorbing potentials combined with a wide a variety of quantum chemistry methods including CCSD(T), SACCI, EOM-CCSD, CASPT2, and NEVPT2. For both Be32- and Mg32-, four low-energy resonance states corresponding to different occupation patterns of the two excess electrons in the two lowest p-σ and p-πorbitals are identified: Two states are dominated by doubly occupied configurations and can be characterized as showing σ and πaromatic character. The other two states correspond to the open-shell singlet/triplet pair. All dianion states are found to be highly unstable and to possess short lifetimes: They show resonance positions in the energy range 2.3-4.3 eV above the ground states of their respective monoanions and broad widths between 1 and 1.5 eV translating into femtosecond lifetimes. For both Be32- and Mg32-, the differences between the four states are small, but the triplet states tend to be slightly more stable than the three singlet states. Thus, in the case of the multicharged ion aromatic character of the excess electrons takes second stage while Coulomb repulsion takes front and center. In addition to the two isolated cluster dianions, model stabilization by small water clusters is explored. Our results show a dramatic drop in resonance position and width corresponding to a lifetime increase by 2 orders of magnitude. However, the "solvated"clusters are still resonances, and a more pronounced perturbation by, for example, yet larger water clusters or a ligand environment providing larger bond dipoles will be needed to fully stabilize two excess electrons localized on a small system such as an alkaline metal trimer.

DOI： 10.1021/acs.jpca.1c00770

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry Letters  

Recently, the analysis of single-orbital entropy and mutual information has been introduced as a tool for the investigation of contributions to the exchange (J) coupling between open-shell metal ions [Stein et al. J. Phys. Chem. Lett. 2019, 10, 6762-6770]. Here, we show that this analysis may lead to an incorrect interpretation of the J-coupling mechanism. Instead, we propose an orbital-entanglement analysis that is based on the two-electron density and that provides a coherent picture of the contributing exchange pathways, which seems fully consistent with the available J values. For this purpose, we used a prototypical bis-μ-oxo binuclear manganese complex ([Mn2O2(NH3)8]4+) and demonstrated that its antiferromagnetism (J < 0), calculated by using the active space composed of all valence pO and dMn orbitals, correlates well with the largest elements in the differential low-spin vs high-spin entanglement map. These elements correspond to interactions between the pairs of dMn orbitals mediated by the oxo-bridging out-of-plane p orbitals, representing the πsuperexchange pathway. We also show that the reduction of active space to manifold of the singly occupied magnetic orbitals does not lead to discrepancy between the calculated J values and entanglement maps. This contrasts to analysis of mutual information, which suggests the "direct"dMn-dMn interactions to play a dominant role for the J coupling, irrespective of the size of active space as well as of the antiferromagnetism expected. The failure is attributed to the large contribution of spin entanglement contained in the mutual information of the low-spin state, which may be regarded as the origin of the different complexity of its wave function and electron density.

DOI： 10.1021/acs.jpclett.0c03652

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Physical Chemistry A  

The fluorescence quantum yield for fluorescent organic molecules is an important molecular property, and tuning it up is desired for various applications. For the computational estimation of the fluorescence quantum yield, the theoretical prediction of the nonradiative decay rate constant has become an attractive subject of study. The rate constant of thermally activated nonradiative decay is related to the activation energy in the photoreaction; thus, the accuracy and reliability of the excited-state potential energies in the quantum chemical computation are critical. In this study, we employed a second-order multireference perturbation wavefunction theory for studying the thermally activated decay via conical intersection (CI) of 1,1-dimethyldibenzo[b,f]silepin derivatives. The correlation between the computed activation energy to reach the CI geometry in the S1 state and the experimentally determined fluorescence quantum yield implied that silepins nonradiatively decay via the CI triggered by the twisting of the central C-C bond. Geometry optimization of the transition state using multireference perturbation theory drastically reduced the estimated activation energy. Our computation gave reasonable predictions of the activation free energies of photoexcited 1,1-dimethyldibenzo[b,f]silepin. The energy profiles and geometry optimizations using proper quantum chemical methods played a critical role in reliable estimation of the rate constant and fluorescence quantum yield.

DOI： 10.1021/acs.jpca.0c08738

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Physical Chemistry Chemical Physics  

A recently introduced framework incorporating the Projector Augmented Wave method and Gauss-type function (GTF-PAW) [X.-G. Xiong and T. Yanai, J. Chem. Theory Comput., 2017, 13, 3236-3249] opens alternative possibilities for performing low-cost molecular computational chemistry calculations. In this work, we present our first attempt to expand the applicability of this method by developing a family of compact general contracted polarization consistent basis sets (PAW-Ln) as an optimized GTF basis in combination with PAW. The results show that PAW-Ln, despite having small numbers of primitives, can provide not only better performance than effective core potential (ECP) but also good accuracy and desirable systematic convergence compared to larger all-electron basis sets. This demonstrates that GTF-PAW using the PAW-Ln basis sets could be a better alternative to both conventional all-electron- A nd ECP-based approaches for routine DFT calculations.

DOI： 10.1039/d0cp05229a

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Theory and Computation  

Determination of excited states of near-infrared (NIR) bioimaging dyes is a challenging theoretical task because of their energy levels with a small gap and the presence of solvation. In the previous study, we showed that the development of the reference interaction site model coupled with the complete active space second-order perturbation theory, the RISM-CASPT2 method, and its extension with the density matrix renormalization group enabled high accuracy prediction of the photochemical properties of bioimaging-related fluorescent molecules in solution (Shimizu et al., J. Chem. Theory Comput. 2018, 14, 5673-5679). This method, however, has a technical issue in convergence of CASSCF optimization, which was encountered when applying the method to a wider variety of systems; thus, practical applications have been hindered. Here, we present an improved scheme of CASSCF optimization with and without the density matrix renormalization group treatment. Detailed derivations and analysis of the second-order orbital optimization scheme with the inclusion of solvation through RISM revealed the requirement of a correction term to the orbital Hessian matrix. As a practical approach, the state-average RISM-CASPT2 method with damping treatment for solvation is presented for improving the convergence of the calculation under reasonable computational cost. The improved scheme allows for performing accurate and numerically stable theoretical analysis of the bioimaging-related excited state with various types of solvation for a P=O-bridged rhodol derivative, which is recently highlighted as a promising photostable NIR dye molecule.

DOI： 10.1021/acs.jctc.9b01289

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Theory and Computation  

The projector augmented wave (PAW) method is a powerful numerical algorithm that serves as a backend, enabling efficient density functional theory (DFT) calculations through the smoothing of valence electronic descriptions. Although it is mainly used in conjunction with plane-wave basis for solid-state systems, its generality permits the combination with other types of basis functions. In the previous study, we proposed a scheme to incorporate the PAW method into the conventional quantum chemical DFT implementation based on Gauss-type function (GTF) basis (Xiong et al., J. Chem. Theory Comput. 2017, 13, 3236-3249). The potentially high usability of the GTF-based PAW method, referred to as GTF-PAW, was previously shown, while its implementation was limited to the local density approximation (LDA). Here, we present a development of two technical extensions in this method toward practical DFT calculations. The GTF-PAW-based formulation and implementation to raise the level of the functional treatment to the generalized gradient approximation (GGA) is presented for improving reliability. In addition, we attempt to use the uniform mesh grid for DFT's quadrature in place of the conventional Becke grid, which was previously used. With the test calculations performed on illustrative molecules, it is confirmed that the conventional approach to implement GGA within GTF basis code can be straightforwardly integrated into the GTF-PAW method, allowing for the numerically stable treatment of the gradients of density. It is demonstrated that the uniform mesh grid can be used as an efficient numerical quadrature approach, which may be advantageous for handling larger systems.

DOI： 10.1021/acs.jctc.0c00137

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Theory and Computation  

We use artificial neural networks (ANNs) based on the Boltzmann machine (BM) architectures as an encoder of ab initio molecular many-electron wave functions represented with the complete active space configuration interaction (CAS-CI) model. As first introduced by the work of Carleo and Troyer for physical systems, the coefficients of the electronic configurations in the CI expansion are parametrized with the BMs as a function of their occupancies that act as descriptors. This ANN-based wave function ansatz is referred to as the neural-network quantum state (NQS). The machine learning is used for training the BMs in terms of finding a variationally optimal form of the ground-state wave function on the basis of the energy minimization. It is relevant to reinforcement learning and does not use any reference data nor prior knowledge of the wave function, while the Hamiltonian is given based on a user-specified chemical structure in the first-principles manner. Carleo and Troyer used the restricted Boltzmann machine (RBM), which has hidden units, for the neural network architecture of NQS, while, in this study, we further introduce its replacement with the BM that has only visible units but with different orders of connectivity. For this hidden-node free BM, the second- and third-order BMs based on quadratic and cubic energy functions, respectively, were implemented. We denote these second- and third-order BMs as BM2 and BM3, respectively. The pilot implementation of the NQS solver into an exact diagonalization module of the quantum chemistry program was made to assess the capability of variants of the BM-based NQS. The test calculations were performed by determining the CAS-CI wave functions of illustrative molecular systems, indocyanine green, and dinitrogen dissociation. The simulated energies have been shown to converge to CAS-CI energy in most cases by improving RBM with an increasing number of hidden nodes. BM3 systematically yields lower energies than BM2, reproducing the CAS-CI energies of dinitrogen across potential energy curves within an error of 50 μEh.

DOI： 10.1021/acs.jctc.9b01132

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Theory and Computation  

Electronic resonances are metastable (N + 1) electron states, in other words, discrete states embedded in an electronic continuum. While great progress has been made for certain types of resonances-for example, temporary anions created by attaching one excess electron to a closed shell neutral-resonances in general remain a great challenge of quantum chemistry because a successful description of the decay requires a balanced description of the bound and continuum aspect of the resonance. Here, a smoothed Voronoi complex absorbing potential (CAP) is combined with the XMS-CASPT2 method, which enables us to address the balance challenge by appropriate choice of the CAS space. To reduce the computational cost, the method is implemented in the projected scheme. In this pilot application, three temporary anions serve as benchmarks: the π∗ resonance state of formaldehyde; the π∗ and σ∗ resonance states of chloroethene as functions of the C-Cl bond dissociation coordinate; and the 4IIu and 2IIu resonance states of N2-. The convergence of the CAP/XMS-CASPT2 results has been systematically examined with respect to the size of the active space. Resonance parameters predicted by the CAP/XMS-CASPT2 method agree well with CAP/SAC-CI results (deviations of about 0.15 eV); however, as expected, CAP/XMS-CASPT2 has clear advantages in the bond dissociation region. The advantages of CAP/XMS-CASPT2 are further demonstrated in the calculations of 4IIu and 2IIu resonance states of N2- including their 3ςu+ and 3δu parent states. Three of the involved states (2IIu3ςu+, and 3δu) possess multireference character, and CAP/XMS-CASPT2 can easily describe these states with a relatively modest active space.

DOI： 10.1021/acs.jctc.9b01032

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

The Complete-Active Space Second-order Perturbation Theory (CASPT2) has been one of the most widely-used methods for reliably calculating electronic structures of multireference systems. Because of its lowest level treatment of dynamic correlation, it has a high computational feasibility; however, its accuracy in some cases falls short of needs. Here, as a simple yet higher-order alternative, we introduce a hybrid theory of the CASPT2 and a multireference variant of the Coupled-Electron Pair Approximation (CEPA), which is a class of high level correlation theory. A central feature of our theory (CEPT2) is to use the two underlying theories for describing different divisions of correlation components based on the full internal contraction framework. The external components, which usually give a major contribution to the dynamic correlation, are intensively described using the CEPA Ansatz, while the rests are treated at the CASPT2 level. Furthermore, to drastically reduce the computational demands, we have incorporated the pair-natural orbital (PNO) method into our multireference implementations. This development, thus, requires highly complex derivations and coding, while it has been largely facilitated with an automatic expression and code generation technique. To highlight the accuracy of the CEPT2 approach and to assess the errors caused by the PNO truncation, benchmark calculations are shown on small- to medium-size molecules, illustrating the high accuracy of the present CEPT2 model. By tightening the truncation thresholds, the PNO-CEPT2 energy converges toward the canonical counterpart and is more accurate than that of PNO-CASPT2 as long as the same truncation thresholds are used.

DOI： 10.1063/1.5142622

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掲載種別：論文集(書籍)内論文   出版者・発行元：Photosynergetic Responses in Molecules and Molecular Aggregates  

In this chapter, we describe our recent development of theoretical approach to analyze photochemisty relevant electronic states (wave functions and energies) for studying photochromic molecules with a promised numerical reliability. Our approach is based on multireference (MR) theory, which is considered to be a critical treatment to properly compute complex electronic structures arising in excited states. It characterizes thewave function by explicitly expressing it as a correlated superposition ofmultiple electronic configurations (or Slater determinants).Wemainly review our recent development of extended multi-state complete active-space second-order perturbation theory incorporated into density matrix renormalization group reference wave functions. Its illustrative applications to molecular photochromic isomerizations, diarylethene derivatives and pentaarylbiimidazole are briefly reviewed in order to show the applicability of our computational approach.

DOI： 10.1007/978-981-15-5451-3_2

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記述言語：英語   出版者・発行元：Plant and Cell Physiology  

The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.

DOI： 10.1093/pcp/pcz183

Open Access

Web of Science

Scopus

PubMed

DOI： 10.1093/pcp/pcz183

Open Access

記述言語：日本語   出版者・発行元：Journal of Chemical Theory and Computation  

For theoretically studying molecules with fluorescence in the near-infrared region, high-accuracy determination of state energy level is required for meaningful analyses since the spectra of interest are of very narrow energy range. In particular, these molecules are in many cases handled in solution; therefore, consideration of the solvation effect is essential upon calculation together with the electronic structure of the excited state. Earlier studies showed that they cannot be described with conventional methods such as PCM-TD-DFT, yielding results far from experimental data. Here, we have developed a new method by combining a solvation theory based on statistical mechanics (RISM) and a multireference perturbation theory (CASPT2) with the extension of the density matrix renormalization group reference states for calculating the photochemical properties of near-infrared molecules and have obtained higher-accuracy prediction.

DOI： 10.1021/acs.jctc.8b00599

Web of Science

Scopus

PubMed

記述言語：英語   出版者・発行元：Journal of Chemical Physics  

We report an efficient algorithm using density fitting for the relativistic complete active space self-consistent field (CASSCF) method, which is significantly more stable than the algorithm previously reported by one of the authors [J. E. Bates and T. Shiozaki, J. Chem. Phys. 142, 044112 (2015)]. Our algorithm is based on the second-order orbital update scheme with an iterative augmented Hessian procedure, in which the density-fitted orbital Hessian is directly contracted to the trial vectors. Using this scheme, each microiteration is made less time consuming than one Dirac-Hartree-Fock iteration, and macroiterations converge quadratically. In addition, we show that the CASSCF calculations with the Gaunt and full Breit interactions can be efficiently performed by means of approximate orbital Hessians computed with the Dirac-Coulomb Hamiltonian. It is demonstrated that our algorithm can also be applied to systems under an external magnetic field, for which all of the molecular integrals are computed using gauge-including atomic orbitals.

DOI： 10.1063/1.5036594

Web of Science

Scopus

PubMed

DOI： 10.1002/poc.3854

DOI： 10.1063/1.5036594

Open Access

DOI： 10.1021/acs.jctc.8b00599

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1038/NCHEM.2784

Web of Science

PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1021/acs.jctc.7b00404

Web of Science

PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1246/cl.170161

Web of Science

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：TAYLOR & FRANCIS LTD  

The Complete Active Space Second-Order Perturbation Theory (CASPT2) is well-established as a high-accuracy electronic structure method. It was originally implemented in the early 1990s to an efficient computer code in the molcas program suite, and this implementation has been extensively used as a standard tool. Here, we report a comparison of it against two independent computer-aided implementations of the CASPT2 method, revealing that the CASPT2 energies provided by the original code of molcas (version 8 or earlier) are inconsistent with the predictions of the lately developed computer-aided implementations. It is shown that this error is associated with the projections of the first-order equation onto the fully internally contracted multireference bases which are partially inconsistent between the left- and right-hand sides. The degree of the errors is assessed by performing illustrative CASPT2 calculations. The errors in total CASPT2 energies are demonstrated to be negligible relative to chemical accuracy in many cases, while there is a difficult case where they may substantially alter chemical description. The incorporation of the consistent projections into molcas has been carried out, which is available in the version 8 sp1.
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DOI： 10.1080/00268976.2016.1271152

Web of Science