Publisher：Chemical Physics Letters  

The coordination-state dependency of the excited-state properties and ultrafast relaxation dynamics from the S2 to the S1 state of bacteriochlorophyll a were analyzed using quantum chemical calculations and nonadiabatic molecular dynamics simulations. TDDFT calculations and orbital analysis clarified the molecular mechanism of the decrease in the excitation energy difference caused by ligand coordination. The results of dynamics simulations also showed that the ligand accelerated the relaxation, and the estimated time constant was in quantitative agreement with the experimental data. We demonstrated the importance of the environmental effects for the relaxation dynamics, which have not been investigated theoretically.

DOI： 10.1016/j.cplett.2023.140669

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Recently reported highly fluorescent 2-phenylbenzo[b]phospholium salt shows an interesting photochemical property. While the counter anion and solvent dependency indicate that the salt is mainly responsible for the absorption and fluorescence spectra, the fluorescence decay clearly depends on the counter anion. In the present study, the detailed mechanism is elucidated using quantum chemical computation and its hybrid with statistical mechanics called 3D-RISM-SCF. Based on the careful exploration of plausible structures of the ion pairs in the methanol and dichloromethane solution, we identify the structure of the charge transfer state, the key on the photoprocess.

DOI： 10.1016/j.molliq.2023.121934

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DOI： 10.1021/acs.jpca.2c08382

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Publisher：Journal of Chemical Physics  

We propose a new hybrid approach combining quantum chemistry and statistical mechanics of liquids for calculating the nuclear magnetic resonance (NMR) chemical shifts of solvated molecules. Based on the reference interaction site model self-consistent field with constrained spatial electron density distribution (RISM-SCF-cSED) method, the electronic structure of molecules in solution is obtained, and the expression for the nuclear magnetic shielding tensor is derived as the second-order derivative of the Helmholtz energy of the solution system. We implemented a method for calculating chemical shifts and applied it to an adenine molecule in water, where hydrogen bonding plays a crucial role in electronic and solvation structures. We also performed the calculations of 17O chemical shifts, which showed remarkable solvent dependence. While converged results could not be sometimes obtained using the conventional method, in the present framework with RISM-SCF-cSED, an adequate representation of electron density is guaranteed, making it possible to obtain an NMR shielding constant stably. This introduction of cSED is key to extending the method's applicability to obtain the chemical shift of various chemical species. The present demonstration illustrates our approach's superiority in terms of numerical robustness and accuracy.

DOI： 10.1063/5.0122326

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Publisher：Science  

Fluorinated analogs of polyhedral hydrocarbons have been predicted to localize an electron within their cages upon reduction. Here, we report the synthesis and characterization of perfluorocubane, a stable polyhedral fluorocarbon. The key to the successful synthesis was the efficient introduction of multiple fluorine atoms to cubane by liquid-phase reaction with fluorine gas. The solid-state structure of perfluorocubane was confirmed using x-ray crystallography, and its electron-accepting character was corroborated electrochemically and spectroscopically. The radical anion of perfluorocubane was examined by matrix-isolation electron spin resonance spectroscopy, which revealed that the unpaired electron accepted by perfluorocubane is located predominantly inside the cage.

DOI： 10.1126/science.abq0516

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DOI： 10.1246/cl.220215

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DOI： 10.1063/5.0092834

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We identified a ternary hybrid catalyst system composed of an acridinium photoredox catalyst, a thiophosphoric imide (TPI) catalyst, and a titanium complex catalyst that promoted an intermolecular addition reaction of organic molecules with various ketones through sp3 C-H bond activation. The thiyl radical generated via single-electron oxidation of TPI by the excited photoredox catalyst abstracted a hydrogen atom from organic molecules such as toluene, benzyl alcohol, alkenes, aldehydes, and THF. The thus-generated carbon-centered radical species underwent addition to ketones and aldehydes. This intrinsically unfavorable step was promoted by single-electron reduction of the intermediate alkoxy radical by catalytically generated titanium(III) species. This reaction provided an efficient and straightforward route to a broad range of tertiary alcohols and was successfully applied to late-stage functionalization of drugs or their derivatives. The proposed mechanism was supported by both experimental and theoretical studies.

DOI： 10.1021/acs.joc.2c00603

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We developed organocatalyst systems to promote the cleavage of stable C-H bonds, such as formyl, α-hydroxy, and benzylic C-H bonds, through a hydrogen atom transfer (HAT) process without the use of exogenous photosensitizers. An electronically tuned thiophosphoric acid, 7,7'-OMe-TPA, was assembled with substrate or co-catalyst N-heteroaromatics through hydrogen bonding and π-π interactions to form electron donor-acceptor (EDA) complexes. Photoirradiation of the EDA complex induced stepwise, sequential single-electron transfer (SET) processes to generate a HAT-active thiyl radical. The first SET was from the electron-rich naphthyl group of 7,7'-OMe-TPA to the protonated N-heteroaromatics and the second proton-coupled SET (PCET) from the thiophosphoric acid moiety of 7,7'-OMe-TPA to the resulting naphthyl radical cation. Spectroscopic studies and theoretical calculations characterized the stepwise SET process mediated by short-lived intermediates. This organocatalytic HAT system was applied to four different carbon-hydrogen (C-H) functionalization reactions, hydroxyalkylation and alkylation of N-heteroaromatics, acceptorless dehydrogenation of alcohols, and benzylation of imines, with high functional group tolerance.

DOI： 10.1021/jacs.2c01705

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DOI： 10.1021/acs.jpcb.2c00326

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

The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in the functionals. Here, we optimize the range-separated parameter, μ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of μ for Chl a and Chl b are smaller than the default value of μ and that for bacteriochlorophyll a, indicating the change in the electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of the solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.

DOI： 10.1063/5.0083395

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

Nitration of benezene was studied with the reference interaction site model-self consistent field method, considering the sulfuric acid solvent. In the bond formation process, the solvation structure drastically changes due to the charge transfer.

DOI： 10.1039/d2cp01699k

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

DOI： 10.1039/d0cp06604d

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

The resonance theory is still very useful in understanding the valence electron structure. However, such a viewpoint is not usually obtained by general-purpose quantum chemical calculations, instead requires rather special treatment such as valence bond methods. In this study, we propose a method based on second quantization to analyze the results obtained by general-purpose quantum chemical calculations from the local point of view of electronic structure and analyze diazadiboretidine and the tautomerization of formamide. This method requires only the "PS"-matrix, consisting of the density matrix (P-matrix) and overlap matrix, and can be computed with a comparable load to that of Mulliken population analysis. A key feature of the method is that, unlike other methods proposed so far, it makes direct use of the results of general-purpose quantum chemical calculations.

DOI： 10.1002/jcc.26703

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26703

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

DOI： 10.1016/j.foodchem.2021.130418

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Publishing type：Research paper (scientific journal)   Publisher：The Japan Institute of Heterocyclic Chemistry  

DOI： 10.3987/com-20-s(k)64

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DOI： 10.1063/5.0010943

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DOI： 10.1063/5.0008903

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DOI： 10.1021/acs.jpcb.9b11080

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DOI： 10.1021/acs.jpcb.9b07456

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We investigate the effects of water addition on a highly stereocontrolled fluorination of dienamine generated by α-branched enals and 6'-hydroxy-9-amino-9-deoxy-epi-quinidine with N-fluorobenzenesulfonimide (NFSI) in the presence of Brønsted acid both experimentally and theoretically. It is experimentally found that water addition to organic solvent significantly shortens the reaction time whereas excessive water addition decreases the enantiomeric excess. The results calculated with three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) method are in good agreement with the experimental ones. It is revealed that the shortness of reaction time is caused by the reactant destabilization and that the decrease in enantiomeric excess is due to the difference of hydration free energy between two transition states.

DOI： 10.3390/molecules24193428

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On our quest for new bioactive molecules from marine sources, two cyclic imines (1, 2) were isolated from a dinoflagellate extract, inhibiting the growth of the respiratory syncytial virus (RSV). Compound 1 was identified as a known molecule portimine, while 2 was elucidated to be a new cyclic imine, named kabirimine. The absolute stereochemistry of 1 was determined by crystallographic work and chiral derivatization, whereas the structure of 2 was elucidated by means of spectroscopic analysis and computational study on all the possible isomers. Compound 1 showed potent cytotoxicity (CC50 < 0.097 µM) against HEp2 cells, while 2 exhibited moderate antiviral activity against RSV with IC50 = 4.20 µM (95% CI 3.31-5.33).

DOI： 10.3390/md17060353

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© 2019 The Royal Society of Chemistry. This chapter describes the important roles of nonclassical C-H hydrogen bonds in asymmetric catalysis. Recently, many asymmetric catalytic reactions have demonstrated that weak C-H hydrogen bond interactions play important roles in selectivity. This chapter introduces the historical background of C-H hydrogen bonds, describes computational analyses of C-H hydrogen bonds in asymmetric catalysis and presents notable examples of asymmetric catalytic reactions in which C-H hydrogen bonds play important roles in selectivity.

DOI： 10.1039/9781788016490-00026

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Magnesium ions (Mg2+) are crucial for various biological processes. A bacterial Mg2+ channel, MgtE, tightly regulates the intracellular Mg2+ concentration. Previous X-ray crystal structures showed that MgtE forms a dimeric structure composed of a total of 10 transmembrane α helices forming a central pore, and intracellular soluble domains constituting a Mg2+ sensor. The ion selectivity for Mg2+ over Ca2+ resides at a central cavity in the transmembrane pore of MgtE, involving a conserved aspartate residue (Asp432) from each monomer. Here, we applied ion-exchange-induced difference FTIR spectroscopy to analyze the interactions between MgtE and divalent cations, Mg2+ and Ca2+. Using site-directed mutagenesis, vibrational bands at 1421 (Mg2+), 1407 (Mg2+), ∼1440 (Ca2+), and 1390 (Ca2+) cm-1 were assigned to symmetric carboxylate stretching modes of Asp432, involved in the ion coordination. Conservative modifications of the central cavity by Asp432Glu or Ala417Leu mutations resulted in the disappearance of the Mg2+-sensitive carboxylate bands, suggesting a highly optimized geometry for accommodating a Mg2+ ion. The dependency of the vibrational changes on Mg2+ and Ca2+ concentrations revealed the presence of a two different classes of binding sites: a high affinity site for Mg2+ ( Kd ≈ 0.3 mM) with low Ca2+ affinity ( Kd ≈ 80 mM), and a medium affinity site for Mg2+ ( Kd ≈ 2 mM) and Ca2+ ( Kd ≈ 6 mM), tentatively assigned to the central cavity and the sensor domain, respectively. With the aid of molecular dynamics simulation and normal-mode analysis by quantum chemistry, we confirm that changes in carboxylate bands of the high affinity binding site originate from Asp432 in the central cavity.

DOI： 10.1021/acs.jpcb.8b07967

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

The energy conversion of oxygenic photosynthesis is triggered by primary charge separation in proteins at the photosystem II reaction center. Here, we investigate the impacts of the protein environment and intramolecular vibrations on primary charge separation at the photosystem II reaction center. This is accomplished by combining the quantum dynamic theories of condensed phase electron transfer with quantum chemical calculations to evaluate the vibrational Huang-Rhys factors of chlorophyll and pheophytin molecules. We report that individual vibrational modes play a minor role in promoting charge separation, contrary to the discussion in recent publications. Nevertheless, these small contributions accumulate to considerably influence the charge separation rate, resulting in subpicosecond charge separation almost independent of the driving force and temperature. We suggest that the intramolecular vibrations complement the robustness of the charge separation in the photosystem II reaction center against the inherently large static disorder of the involved electronic energies.

DOI： 10.1021/acs.jpclett.8b02119

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Publisher：Elsevier {BV}  

DOI： 10.1016/j.chemphys.2018.03.012

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Society of Chemical Engineers, Japan  

DOI： 10.1252/jcej.17we288

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Language：English   Publisher：Elsevier B.V.  

Background Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. Scope of review We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. Major conclusions The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. General significance These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled “Biophysical Exploration of Dynamical Ordering of Biomolecular Systems” edited by Dr. Koichi Kato.

DOI： 10.1016/j.bbagen.2017.10.001

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Institute of Physics Inc.  

The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations
the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.

DOI： 10.1063/1.5009785

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DOI： 10.2477/jccj.2018-0006

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Biochemistry and Molecular Biology Inc.  

Canonical K channels are tetrameric and highly K-selective, whereas two-pore– domain K (K2P) channels form dimers, but with a similar pore architecture. A two-pore– domain potassium channel TWIK1 (KCNK1 or K2P1) allows permeation of Na and other monovalent ions, resulting mainly from the presence of Thr-118 in the P1 domain. However, the mechanistic basis for this reduced selectivity is unclear. Using ion-exchange–induced difference IR spectroscopy, we analyzed WT TWIK1 and T118I (highly K-selective) and L228F (substitution in the P2 domain) TWIK1 variants and found that in the presence of K ions, WT and both variants exhibit an amide-I band at 1680 cm1. This band corresponds to interactions of the backbone carbonyls in the selectivity filter with K, a feature very similar to that of the canonical K channel KcsA. Computational analysis indicated that the relatively high frequency for the amide-I band is well explained by impairment of hydrogen bond formation with water molecules. Moreover, concentration-dependent spectral changes indicated that the K affinity of the WT selectivity filter was much lower than those of the variants. Furthermore, only the variants displayed a higher frequency shift of the 1680-cm1 band upon changes from K to Rb or Cs conditions. High-speed atomic force microscopy disclosed that TWIK1’s surface morphology largely does not change in K and Na solutions. Our results reveal the local conformational changes of the TWIK1 selectivity filter and suggest that the amide-I bands may be useful “molecular fingerprints” for assessing the properties of other K channels.

DOI： 10.1074/jbc.RA118.001817

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

The vibrational dynamics of SCN in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong. (C) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2017.03.008

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

Two new sesterterpenoids, 1 and 2, were isolated from the sponge Luffariella variabilis. Their planar structures were characterized with spectroscopic analyses. The sole chiral center of compound 1 was elucidated as 12R by comparing observed and calculated optical rotation values. The configurations of compound 2 were determined by NMR and electronic circular dichroism (ECD) studies. Furthermore, compound 2 showed cytotoxicity at IC50 1.0 mu M against NBT-T2 cells.

DOI： 10.3390/md15080249

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We investigate the photoexcitation dynamics of [Cu(phen)(2)](+) (phen = 1,10-phenanthroline) in solutions by using the molecular mechanics with Shepard interpolation method, which enables us to generate potential energy surfaces of the Cu complex efficiently. The calculated flattening rates and coherent vibration motions are in good agreement with the experimental results. We find that the photoexcitation dynamics in the gas phase is much different from those in solutions, which indicates the importance of the solvent effects on the photoexcitation dynamics. (C) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2017.04.082

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

Fluorination of dienamines generated by alpha-branched enals and 6'-hydroxy-9-amino-9-deoxy-epi-quinidine (30 mol %) with NSFI show excellent alpha-regioselectivity to construct allylic fluorides containing a highly stereocontrolled quaternary fluorinated carbon (E/Z &gt;= 20/1 and up to 93% enantiometric excess (ee)). By DFT calculation, the quinuclidine moiety of the catalyst was shown to function as a coordinating group to promote a reaction at the proximal alpha-position, and the nonclassical CH hydrogen bond plays an important role in the high enantioselectivity.

DOI： 10.1021/acscatal.7b01178

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

Bioassay-guided separation of a lipophilic extract of the crinoid Alloeocomatella polycladia, inhibiting the activity of HCV NS3 helicase, yielded two groups of molecules: cholesterol sulfate and four new aromatic sulfates 1-4. The structures of the aromatics were elucidated by spectroscopic analysis in addition to theoretical studies. The aromatic sulfates 1-4 showed moderate inhibition against NS3 helicase with IC50 values of 71, 95, 7, and 5 mu M, respectively.

DOI： 10.3390/md15040117

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Language：English   Publishing type：Part of collection (book)   Publisher：ANNUAL REVIEWS  

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

DOI： 10.1146/annurev-physchem-052516-050827

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

The molecular recognition process of the carbohydrate-binding module family 36 (CBM36) was examined theoretically. The mechanism of xylan binding by CBM36 and the role of Ca2+ were investigated by the combined use of molecular dynamics simulations and the 3D reference interaction site model method. The CBM36 showed affinity for xylan after Ca2+ binding, but not after Mg2+ binding. Free-energy component analysis of the xylan-binding process revealed that the major factor for xylan-binding affinity is the electrostatic interaction between the Ca2+ and the hydroxyl oxygens of xylan. The van der Waals interaction between the hydrophobic side chain of CBM36 and the glucopyranose ring of xylan also contributes to the stabilization of the xylan-binding state. Dehydration on the formation of the complex has the opposite effect on these interactions. The affinity of CBM36 for xylan results from a balance of the interactions between the binding ion and solvents, hydrophilic residues around xylan, and the hydroxyl oxygens of xylan. When CBM binds Ca2+, these interactions are well balanced; in contrast, when CBM binds Mg2+, the dehydration penalty is excessively large.

DOI： 10.1088/0953-8984/28/34/344005

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

The reaction with beta-trifluoromethyl acrylamide 3e and azomethine ylides generated from L-proline and several aldehydes provided the corresponding trifluoromethylated pyrrolizidines with excellent diastereoselectivity (&gt;20/1) in all cases and moderate regioselectivity (up to 1/5.9). A DFT calculation was also examined to reveal the origin of these stereoselectivities. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jfluchem.2016.07.013

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

Potential energy profiles and electronic structural interpretation of the CO and H-2 binding reactions to molybdenocene and tungstenocene complexes [MCp2] (M = Mo and W, Cp = cycropentadienyl) were studied using density functional theory calculations and ab initio multiconfigurational electronic structure calculations. Experimentally observed slow H-2 binding was reasonably explained in terms of the spin-blocking effect. Electronic structural analysis at the minimum-energy intersystem crossing point (MEISCP) revealed that the singly occupied molecular orbital's pi-bonding/sigma-antibonding character in the M-CO/H-2 moiety determines the energy levels of the MEISCP. Analysis of the reaction coordinate showed that the singlet-triplet gap significantly depends on the Cp-M-Cp angle. Therefore, not only the metal ligand distance but also the Cp-M-Cp angle is an important reaction coordinate to reach the MEISCP, the transition state of H-2 binding. The role of spin orbit coupling is also discussed.

DOI： 10.1021/acs.inorgchem.6b01187

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

We develop an efficient method to generate an accurate semiglobal potential energy surface of a molecule in condensed phases with low computational cost. We apply the method to the calculation of the site energies and their fluctuations of bacteriochlorophyll (BChl) a pigments in the Fenna-Matthews-Olson (FMO) complex using the density functional properly describing the ground and excited states of BChl a in solutions in our previous work (J. Phys. Chem. B 2014, 118, 10906-10918). The errors of the potential energies calculated from the present and QM/MM methods are small: similar to 1 kcal/mol for both the ground and excited states. The calculated site energies are in good agreement with the experimentally fitted results. The calculated spectral density also agrees with the experimentally available data. The spectral densities of BChl 2 and BChl 5 are much larger than those of the other five sites. The present method is expected to provide new insights into the efficient excitation energy transfer in light-harvesting antennas.

DOI： 10.1021/acs.jctc.6b00516

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

A new trinor-guaiane sesquiterpene has been isolated from an Indonesian soft coral Anthelia sp. The planar structure, possessing an octahydroazulene skeleton, and relative stereochemistry were established by analyzing 1D and 2D NMR data, including NOB experiments. Its absolute stereochemistry was elucidated to be IS, 48, 7R, and lOR by comparing observed and calculated optical rotation values. The new compound showed weak cytotoxicity against NBT-T2 cells.

DOI： 10.1177/1934578x1501001124

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

The excited-state properties of bacteriochlorophyll (BChl) a in triethylamine, 1-propanol, and methanol are investigated with the time-dependent density functional theory by using the quantum mechanical and molecular mechanical reweighting free energy self-consistant field method. It is found that no prevalent density functionals can reproduce the experimental excited-state properties, i.e., the absorption and reorganization energies, of BChl a in the solutions. The parameter mu in the range-separated hybrid functional is therefore optimized to reproduce the differences of the absorption energies in the solutions. We examine the origin of the differences of the absorption energies in the solutions and find that sensitive balance between contributions of structural changes and solute-solvent interactions determines the differences. The accurate description of the excitation with the density functional with the adjusted parameter is therefore essential to the understanding of the excited-state properties of BChl a in proteins and also the mechanism of the photosynthetic systems.

DOI： 10.1021/jp507259g

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We calculate the free energy profile for the postulated hydride transfer reaction mechanism for the catalysis of lysine demethylation by lysine-specific demethylase LSD1. The potential energy surface is obtained by using combined electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) and single-configuration molecular mechanics (MM). We employ a constant valence bond coupling term to obtain analytical energies and gradients of the EE-MCMM subsystem, which contains 45 quantum mechanics (QM) atoms and which is parametrized with density functional calculations employing specific reaction parameters obtained by matching high-level wave function calculations. In the MM region, we employ the Amber ff03 and TIP3P force fields. The free energy of activation at 300 K is calculated by molecular dynamics (MD) umbrella sampling on a system with 102 090 atoms as the maximum of the free energy profile along the reaction coordinate as obtained by the weighted histogram analysis method with 17 umbrella sampling windows. This yields a free energy of activation of only 10 kcal/mol, showing that the previously postulated direct hydride transfer reaction mechanism is plausible, although we find that it is better interpreted as a concerted transfer of a hydrogen atom and an electron.

DOI： 10.1021/jp404292t

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

The vibrational energy relaxations (VERs) of the CO stretching mode of acetone and its complexes with alcohols are investigated by sub-picosecond pump-probe spectroscopy and molecular dynamics simulation. The time constants of the vibrational energy relaxation of the free acetone and that of the 1:1 complex are 4.4 and 2.3 ps for methanol solvent and 5.2 and 1.8 ps for 1-proponal solvent, respectively. The VER rate is accelerated a few times by formation of the hydrogen bond. This acceleration of the vibrational energy relaxation is successfully reproduced by the Landau-Teller method calculated from the molecular dynamics simulation. Molecular dynamics simulations reveal that the VER time of acetone with the hydrogen bond is largely affected by the solute polarization induced by solvent molecules.

DOI： 10.1021/jp310621p

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

We investigate an ultrafast excited-state intramolecular proton transfer (ESIPT) reaction and the subsequent coherent vibrational motion of 10-hydroxybenzo[h]quinoline in cyclohexane by the electronically embedded multiconfiguration Shepard interpolation method, which enables us to generate the potential energy surface of the reaction effectively and thus carry out a direct excited-state dynamics simulation with low computational costs. The calculated time scale of the ESIPT and the frequencies and lifetimes of coherent motions are in good agreement with the experimental results. The present study reveals that the coherent motions are caused by not only the proton transfer itself but also the backbone displacement induced by the ESIPT. We also discuss the effects of the solvent on the dynamics of the coherent vibrational modes.

DOI： 10.1021/jz201042u

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

Density functional theory is a powerful and efficient method for calculating potential energy surfaces for chemical reactions, but its application to complex systems, such as reactions in enzymes, is often prohibitively expensive, even when high-level theory is applied only to a primary subsystem, such as an active site, and when the remaining system is treated by molecular mechanics. Here we show how the combination of multiconfiguration molecular mechanics with charge response kernels can speed up such calculations by three or more orders of magnitude. The resulting method, called electrostatically embedded multiconfiguration molecular mechanics, is illustrated by calculating the free energy of activation profile for the dehalogenation of 1,2-dichloroethane by haloalkane dehalogenase. This shows how hybrid density functionals or other high-level electronic structure methods can now be used efficiently in simulations that require extensive sampling, such as for calculating free energy profiles along a high-barrier reaction coordinate.

DOI： 10.1021/ct900301d

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

We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl- + CH3Cl' -&gt; ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level.,The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and-MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.

DOI： 10.1021/ct8000816

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

We present a new method for generating global or semiglobal potential energy surfaces in the presence of an electrostatic potential; the new method can be used to model chemical reactions in solution or in an enzyme, nanocavity, or other chemical environment. The method extends the multiconfiguration molecular mechanics method so that the energy depends on the electrostatic potential at each atomic center. The charge distribution of the system can also be calculated. We illustrate the method by applying it to the symmetric bimolecular reaction Cl(-)+CH3Cl&apos;-&gt; ClCH(3)+Cl&apos;(-) in aqueous solution, where the potential energy information is obtained by the combined density functional and molecular mechanical method, that is, by the combined quantum mechanical and molecular mechanical method (QM/MM) with the QM level being density functional theory. It is found that we can describe a semiglobal potential energy surface in aqueous solution with electronic structure information obtained entirely in the gas phase, including the linear and quadratic responses to variations in the electrostatic potential distribution. The semiglobal potential energy surface calculated by the present method is in good agreement with that calculated directly without any fitting.

DOI： 10.1021/ct800004y

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

The transition state on the free energy surface for Claisen rearrangement of chorismate in Bacillus subtilis chorismate mutase is calculated with a method based on a linear response theory. The calculated activation free energy is 16.9 kcal/mol, which is in good agreement with the experimental one. The catalytic ability of the enzyme is examined by comparing the activation barrier with that in aqueous solution and found to be mainly attributed to the conformational restriction of the substrate. We also calculate the kinetic isotope effects, which are in accord with the experimental estimates. (c) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.02.044

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

The authors present a method based on a linear response theory that allows one to optimize the geometries of quantum mechanical/molecular mechanical (QM/MM) systems on the free energy surfaces. Two different forms of linear response free energy functionals are introduced, and electronic wave functions of the QM region, as well as the responses of electrostatic and Lennard-Jones potentials between QM and MM regions, are self-consistently determined. The covariant matrix relating the QM charge distribution to the MM response is evaluated by molecular dynamics (MD) simulation of the MM system. The free energy gradients with respect to the QM atomic coordinates are also calculated using the MD trajectory results. They apply the present method to calculate the free energy profiles of Menshutkin-type reaction of NH3 with CH3Cl and Claisen rearrangement of allyl vinyl ether in aqueous solution. For the Menshutkin reaction, the free energy profile calculated with the modified linear response free energy functional is in good agreement with that by the free energy perturbation calculations. They examine the nonequilibrium solvation effect on the transmission coefficient and the kinetic isotope effect for the Claisen rearrangement. (c) 2007 American Institute of Physics.

DOI： 10.1063/1.2715941

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

Electronic structures of [Fe2S2(SCH3)(4)](2-.3-) in DMSO solution are calculated using reference interaction site model complete active space self-consistent field (RISM-CASSCF)/multireference second-order Moller-Plesset perturbation theory (MRMP) method. For the reduced state, we obtain both the low-spin Fe3+Fe2+ localized and high-spin Fe2.5+Fe2 5+ delocalized forms, which are very close in energy. The spin interaction constants obtained from the energies of states with various spin multiplicities are in good agreement with the available experimental estimates both for the oxidized and for the reduced states. The dynamic electron correlation effect is found to be important in estimating the spin interaction between the Fe ions. The redox potentials are calculated to be 2.87 and 2.78 eV for the localized and delocalized reduced states, respectively, which are close to the experimental values. We devise a simple model for calculating the free energy curves of the reduction process based on the RISM-SCF theory. The activation barrier height is calculated to be 7.4 kcal/mol at the equilibrium geometry of oxidized state, indicating that the reduction reaction will occur efficiently in DMSO solvent. The effect of solvent fluctuation on the free energy profiles is discussed on the basis of the present calculations.

DOI： 10.1021/jp0581429

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