Search

The fully optimized geometrical structures of the CaMn4Ox (x = 5, 6) clusters in the Si (i = 0–3) states of the Kok cycle of photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics (QM/MM) calculations were compared to recent experimental results based on serial femtosecond crystallography (SFX). The Mn Mn and Ca Mn distances obtained by the QM/MM calculations were found to be totally comparable to the SFX experiments, elucidating the entire Kok cycle involving the S4 transition state during the O O bond formation for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII).

The reaction mechanism of the non-enzymatic stereoselective formation of the (3S, 3aS, 7aR) configuration of the wine lactone from the (6R) form of (E)-8-carboxylinalool in acidic aqueous solution was analyzed by quantum chemistry calculations. The transition states for the cyclization and hydride shift of the carbocation intermediates were obtained (

Accepted: 2018-10-31, 資料番号: SA1180244000

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O–O sigma bond formation.

Free energy calculations are indispensable for characterizing the conformational transitions of proteins. The dominant transition path can be regarded as a minimal free energy path (MFEP) on a free energy landscape (FEL). However, it takes computational costs to find an MFEP. In this study, we propose a post-process to estimate an approximated MFEP. In our method, an initial string consisting of beads is generated and relaxed using local centroids on the pre-prepared FEL to estimate the MFEP. The implementation in Python is available as a jupyter notebook from the website https://github.com/riquri/post-string .

As a possible formation mechanism of glycine in astrophysical environments, a reaction path via aminoacetonitrile and hydantoin (2,4-imidazolidinedione), which have been detected in an interstellar cloud and meteorites, respectively, were analyzed using the density functional theory. The formation of hydantoin from aminoacetonitrile via the Bucherer-Bergs reaction and the hydrolysis of hydantoin were investigated. The results showed that the catalytic water molecules significantly lower the reaction barriers for the formation of hydantoin. Although the highest barrier is still too high that the pathway is inactive in an interstellar medium, this reaction would proceed during the heating of the meteorite parent body.

Solvent effects on the quenching process from the first excited state of 5-(1-pyrenyl)-2⿲-deoxyuridine (Py-dU) were theoretically examined. Our results suggest that the excited-state electron transfer occurs without the so-called proton-coupled electron transfer process, which supports experimental results. Although there are no remarkable differences observed in the structure and the corresponding S 1 excitation energy between the solutions of MeOH and MeCN within a polarizable continuum model, we report here that hydrogen bonds between the explicit MeOH molecule with the dU moiety, whose structure was frequently found in molecular dynamics simulations, result in an enhancement of the electron-transfer rate constant.

As a strategy for reproducing rare, biologically important events, we previously developed the Outlier FLOODing (OFLOOD) method [J. Comput. Chem. 36 (2015) 97–102]. This method utilizes conformational resampling from rarely occurring states, detected as outliers, to promote conformational transitions relevant to the rare events. However, to perform OFLOOD efficiently requires specifying a set of appropriate reaction coordinates (RCs) with non-trivial specifications. Therefore, in this paper, we propose a strategy to obtain a set of appropriate RCs using a method where the best set of RCs are automatically searched from the initially given RCs, via clustering the states of biomolecules.

Computational costs with the use of the initial guesses formed by the divide-and-conquer approach are examined. For conventional density functional theory calculations, their computational costs rapidly increase as the system sizes increase, therefore, an efficient methodologies to construct a fine initial molecular orbital guess or a fine density matrix (DM) is quite variable in order to enhance the fast convergence. We examined the DM construction approaches by changing the subsystem buffer sizes and number of divisions, and their computational costs were numerically investigated in order to clarify their characteristic features.

Sampling of biologically important rare events are indispensable for understanding biological functions. As a rare event search method, we have developed TaBoo SeArch algorithm (TBSA), in which states of bio-molecules with low frequency are intensively resampled via short-time molecular dynamics simulations with reference to an inverse histogram projected on a reaction coordinate as a weight in random searches. The one-dimensional inverse histogram is extended herein to a multi-dimensional form as a function of appropriate reaction coordinates. Due to the extension with a restriction on sampled spaces, the protein-folding processes of a chignolin in explicit solvent environment are more efficiently reproduced.

Four possible reaction paths of an Fe-containing nitrile hydratase (NHase) are examined using the method of hybrid quantum mechanics/molecular mechanics (QM/MM) to reveal the initial steps of the catalytic mechanism of NHases. The reaction barrier for a nucleophilic attack of the sulfenic oxygen of αCys114-SO− to the substrate is the lowest among the four paths, though another path, in which a water molecule activated by αCys114-SO− attacks the substrate, also has a low enough barrier. Under the protein environment, βArg56 has weaker proton donor ability and shows no proton transfer to αCys114-SO−, which was reported in model clusters.

We apply the non-empirical parameter tuning method proposed by Baer et al. to the CAM-B3LYP functional for the excitation energies of photochromic diarylethene derivatives in the closed- and open-ring isomers. Using the tuned parameter set, the time-dependent density functional theory calculations are found to well reproduce the experimental UV–Vis spectra with the same quality as our previous calculations with the parameter set obtained by referring the experimental values. These results demonstrate the performance of this parameter tuning method in the CAM-B3LYP functional for the excitation energies of unknown systems without any experimental data.

The Cu A site is the electron mediator in cytochrome c oxidase (C c O), providing an appropriate electronic structure for rapid electron transfer. We have studied the coordinating effects of His, Met, and the peptide carbonyl group of Glu of the Cu A site, using the density functional theory. Our computation demonstrates that the His ligation provides strong orbital and electrostatic effects on the electronic structure of the Cu A site, while that the Met coordination gives weak orbital and electrostatic effects. A coordination of the peptide carbonyl group affects the electronic structure of the Cu A site only electrostatically.

The range separating parameter (μ) in the long-range corrected spin-unrestricted BLYP (LC-UBLYP) method is tuned so as to reproduce the second hyperpolarizabilities (γ) of several open-shell singlet metal–metal bonded systems calculated using the strongly electron-correlated spin-unrestricted coupled cluster singles, doubles and perturbative triples [UCCSD(T)] method. For these systems, μ values ranging between 0.7 and 0.9 bohr−1 provide a reliable description of the bond length dependence of γ in the bond length region where γ is enhanced by the contribution of dσ electrons with an intermediate open-shell character.

In order to understand roles of E168 and Y170 residues in loop-segment (N166–V177) of nylon-6 byproduct-degrading enzymes, we determined substrate-binding structures of E168Q and Y170F mutants using molecular dynamics simulation with in silico mutations. We found that movement of the loop-segment plays key roles not only in allowing the substrate to be bound by induced fit mechanism but also in forming water-exclusive environment. Fluctuations of the loop-segment in the mutant enzymes caused a room near the catalytic site, where water molecules can access. We propose that the water located exclusivity at the catalytic site is a major factor of its activity.

We have introduced a new computational method to provide an acid dissociation constant (p K a ) value of an imino-proton in 5-substituted uracil. A linear fitting is applied to the experimentally observed p K a to compute the Gibbs energy difference of a deprotonation reaction by a conductor-like polarizable continuum model (CPCM)-B3LYP/aug-cc-pVDZ level of theory. Despite its simplicity in our method for evaluating p K a , the error falls within 0.5 p K a units except for X = O − (X: ligand of C5). The predicted p K a values for other 5-substituted uracils are also found to agree well with experimental data.

To demonstrate the performance of a novel approximate spin-projected (ASP) spin-unrestricted density functional theory (UDFT) method, we examine the diradical character dependences of the static polarizability (α) and second hyperpolarizability (γ) of a model open-shell singlet molecule, p-quinodimethane (PQM), using several hybrid and long-range corrected (LC) exchange–correlation functionals. The ASP-LC-UBLYP method with a range-separating parameter μ = 0.47 is found to reproduce semi-quantitatively the diradical character dependences of α and γ of the PQM model calculated using the strongly-correlated UCCSD(T) method.

Geometrical and electronic structures of uracil nucleobase pair containing Ag I ions have been studied theoretically and computationally. Four stable conformers are expected to co-exist under normal experimental conditions, and transition state structures among the conformers are also presented. The replacement of protons with Ag I ions increases the size of the mismatch nucleobase pairs and leads to a better match of the size stabilizing the duplex. From the calculated infrared, Raman and UV absorption spectra of each conformer and mixtures of all conformers, all the conformers are expected to make significant contributions to the experimental spectroscopic profiles.

The stabilities of products for proton-transfer reactions in stacked two guanine(G)–cytosine(C) pairs are discussed by means of Hartree–Fock, MP2 and density functional methods. The stacking energy of the original 5′-d(CpG)-3′ (CG/GC) differs from that of single proton-transfer (SPT) product. On the other hand, the stacking energy of the original 5′-d(GpG)-3′ (GC/GC) is essentially equal to the double proton-transfer (DPT) products. The dispersion forces of both CG/GC and its SPT product are similar to each other. Not only dispersion force but also Coulomb attraction contributes to the stability of the SPT product of CG/GC.

The quantal cumulant dynamics (QCD) method for multi-dimensional cases is developed in order to simulate the model quantum confinement systems under a magnetic field. We feature the resonant levels in quantum wells as found in the classical mechanics, magnetic-field induced tunneling, and magnetic confinement in a model quantum ring nanostructure. Trajectories and position cumulant variables are analyzed in order to characterize these phenomena. We find that (i) the magnetic confinement originates from resonant level trajectories between cycloid and drift motions and (ii) the position cumulant variables decrease during transitions among the wells, which reflects a tunneling motion.

application/pdf, The applicability of time-reversible integrators to the recently developed quantal cumulant dynamics (QCD) is examined, and their accuracy and efficiency are demonstrated by comparison with the Runge-Kutta method. We proposed three schemes, which differ in their partitions and orders of an exponential function of a Liouvillian. Three-part partition conserves the total energy with sufficient accuracy, whereas the two-part one does not. It is found that the equations of motion of the QCD are sensitive to the order. The sensitivity is due to the accordance of fractional time in variables, which contribute to the total energy, after the propagation.

An efficient molecular dynamics methodology, which is suitable for analyzing molecular vibrations of molecules with many degrees of freedom, is presented. The framework of the methodology consists of two main elements. First, a mixed quantum-classical dynamics method is utilized to incorporate quantum effects of nuclei. Second, an approximation of potential energy surface is introduced. The theoretical background, stability of the simulation and the correspondence with quantum simulation are discussed. The accuracy of the methodology over ordinary classical dynamics is described with numerical examples as well.

Energetic and structural changes in the hydrogen bonds of guanine (G) and cytosine (C) base pair due to Pt complex binding are investigated by post-Hartree–Fock methods. When the ligands are NH 3 or H 2 O, the structure undergoes intermolecular proton transfer from G to C (denoted as G ∗ C pair) resulting in an increase in the bonding energy of 3–10 kcal/mol. This renders the structure to be metastable due to: (a) successive processes of charge transfer from G to cisplatin thereby stabilizing the GC and G ∗ C pairs and (b) an additional hydrogen bond between G and the ligand of Pt atom.

We report here the finding by means of visible-near IR absorption and near-IR fluorescence spectroscopies and atomic force microscopy that a total aromatic polyimide has a high potential to solubilize single-walled carbon nanotubes (SWNTs) individually in organic solutions. The solutions contained SWNTs having (7, 6), (7, 5), (8, 4), (9, 5) and (8, 6) indices. With the increasing concentrations of SWNTs, the solutions became viscous and then changed to gels that exhibited characteristic spectral features of individually dissolved SWNTs.