Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

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.

DOI： 10.1039/d3cp01723k

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Molecular wavefunction encoded with artificial neural networks (BM2, BM3, and RBM) is prepared by the quantum algorithm.

DOI： 10.1039/d2dd00093h

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

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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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202219107

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.2c03619

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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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/5.0135257

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acschembio.2c00771

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.2c07299

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

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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Other Link： https://academic.oup.com/pcp/article-pdf/63/11/1720/47195497/pcac127.pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.xcrp.2022.101045

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

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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Other Link： https://www.nature.com/articles/s41598-022-19375-2

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

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 S_N2 reaction in a single-walled carbon nanotube reaction field.

DOI： 10.1063/5.0094777

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DOI： 10.1021/acscatal.2c02233

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

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 (Φ_F >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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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202201965

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

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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Other Link： https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0091973/16543411/224102_1_online.pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsomega.2c02822

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

A free-base 5-thiaporphyrinium cation and its zinc complex were synthesised and their excited state dynamics were investigated experimentally and theoretically.

DOI： 10.1039/d2cc00522k

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.1c13610

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CiNii Research

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

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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Other Link： https://academic.oup.com/pcp/article-pdf/63/4/450/43396790/pcac011.pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.1c08504

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacsau.1c00417

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.1c05944

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.1c04457

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

The use of donor-pi-acceptor (D-pi-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) pi-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. lambda(em) = 704 nm and phi(F) = 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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.1c00770

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.0c03652

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DOI： 10.1021/acs.jpca.0c08738

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

<p>A new family of polarization consistent basis set, combined with the projector augmented wave method, was introduced. The basis sets are compact and have good performance as compared to conventional all-electron basis sets in DFT calculations.</p>

DOI： 10.1039/d0cp05229a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.9b01289

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.0c00137

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

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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Scopus

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.9b01032

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.5142622

Open Access

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PubMed

Publishing type：Part of collection (book)   Publisher：Springer Singapore  

DOI： 10.1007/978-981-15-5451-3_2

Scopus

Language：English   Publisher：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

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PubMed

DOI： 10.1093/pcp/pcz183

Open Access

Language：Japanese   Publisher：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

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PubMed

Language：English   Publisher：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

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PubMed

DOI： 10.1002/poc.3854

DOI： 10.1063/1.5036594

Open Access

DOI： 10.1021/acs.jctc.8b00599

Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Singlet fission, in which a singlet exciton is converted to two triplet excitons, is a process that could be beneficial in photovoltaic applications. A full understanding of the dynamics of singlet fission in molecular systems requires detailed knowledge of the relevant potential energy surfaces and their (conical) intersections. However, obtaining such information is a nontrivial task, particularly for molecular aggregates. Here we investigate singlet fission in rubrene crystals using transient absorption spectroscopy and state-of-the-art quantum chemical calculations. We observe a coherent and ultrafast singlet-fission channel as well as the well-known and conventional thermally assisted incoherent channel. This coherent channel is accessible because the conical intersection for singlet fission on the excited-state potential energy surface is located very close to the equilibrium position of the ground-state potential energy surface and also because of the excitation of an intermolecular symmetry-breaking mode, which activates the electronic coupling necessary for singlet fission.

DOI： 10.1038/NCHEM.2784

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The Projector Augmented Wave (PAW) method developed by Blochl is well recognized as an efficient, accurate pseudopotential approach in solid-state density functional theory (DFT) calculations with the plane-wave basis. Here we present an approach to incorporate the PAW method into the Gauss-type function (GTF) based DFT implementation, which is widely used for molecular quantum chemistry calculations. The nodal and high-exponent GTF components of valence molecular orbitals (MOs) are removed or pseudized by the ultrasoft PAW treatment, while there is elaborate transparency to construct an accurate and well-controlled pseudopotential from all-electron atomic description and to reconstruct an all-electron form of valence MOs from the pseudo MOs. The smoothness of the pseudo MOs should benefit the efficiency of GTF-based DFT calculations in terms of elimination of high-exponent primitive GTFs and reduction of grid points in the numerical quadrature. The processes of the PAW method are divided into basis-independent and -dependent parts. The former is carried out using the previously developed PAW libraries LIBPAW and ATOMPAW. The present scheme is implemented by incorporating LIBPAW into the conventional GTF-based DFT solver. The details of the formulations and implementations of GTF-related PAW procedures are presented. The test calculations are shown for illustrating the performance. With the near-complete GTF basis at the cc-pVQZ level, the total energies obtained using our PAW method with suited frozen core treatments converge to those with the conventional all-electron GTF-based method with a rather small absolute error.

DOI： 10.1021/acs.jctc.7b00404

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：CHEMICAL SOC JAPAN  

Theoretical schemes to evaluate electronic coupling elements for triplet-triplet annihilation (TTA) processes are proposed using fragment molecular orbital-linear combination of molecular orbital methods. Combining them with the Marcus formula, we estimate rate constants of TTA for 9,10-diphenylanthracene (DPA). We also performed molecular dynamics simulations of diffusion of DPAs in solution to estimate rate constants of molecular encounter in an assumed diffusion-controlled reaction. On the basis of the calculated rate constants, the mechanism of TTA process for DPAs in solution are discussed.

DOI： 10.1246/cl.170161

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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

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