Kazuto Nakata

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water.

The cis-trans isomerization of the peptide bond preceding a proline plays important roles in protein folding and biological function. Although many experimental and theoretical studies have been done, the mechanism has not yet been clearly elucidated. We studied the cis-trans isomerization of the proline dipeptide (Ace-Pro-NMe) in explicit water by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. We obtained the free energy landscape during the isomerization by using the umbrella sampling method. The free energy landscape is in good accordance with previous experimental and theoretical values. We observed that in the middle of the isomerization, the prolyl nitrogen transiently takes pyramidal conformations in two polarized directions and that, simultaneously, the prolyl C-N bond extends. We show that these geometrical changes cooperatively transform the prolyl nitrogen from a sp(2)-hybridized electronic state into a sp(3)-hybridized one, and thus realize a transition state that reduces the rotational barriers separating the cis- and trans-states. We also found that the hydration of the prolyl nitrogen stabilizes the negative pyramidal conformation, while an intramolecular interaction mainly stabilizes the positive one. Fluctuations in the polarity and magnitude of the pyramidal conformation during the isomerization are interpreted as a competition between the hydrogen-bonding partners for the prolyl nitrogen between different sides of the pyrrolidine ring.

A CAS-DFT study of fundamental degenerate and nearly degenerate systems

We present simple CAS-DFT approaches for degenerate and nearly degenerate systems. In this method, we do not employ any auxiliary variables, but employ the effective CASCI-DFT and CASSCF-DFT equations for the ground and excited states. Simple applications for fundamental systems such as atomic multiplet states (C, N+n , and O+n ), the transition metal complex V(III)L6 (L = H2O and CO) and the Cu(II) acetate dimer Cu(II)2(Ac)4(H2O)2 are presented. The results are discussed from the viewpoint of the shapes of the potential curves of several nearly degenerate spin states, the theory of molecular magnetism and the reliability of the CAS space employed. The computational results are fully compatible with the experimental results available, and also with those of ligand field theory.

Numerical Simulations of Large-Scale Sediment Transport Caused by the 2011 Tohoku Earthquake Tsunami in Hirota Bay, Southern Sanriku Coast

A numerical sediment transport model (STM) was used to investigate coastal geomorphic changes that resulted from the 2011 Tohoku earthquake tsunami in Rikuzentakata City and Hirota Bay on the southern Sanriku Coast of Japan. The simulation was verified using observed inundation processes and heights, measured topographic changes and sediment deposition. Aerial video footage recorded by the Iwate Prefectural Police was also used. The results show that the numerical model was able to predict the spatial distribution and volume of erosion and deposition in Hirota Bay, as well as sediment transport processes. The effects of sediment transport on tsuneimi inundation were also investigated. Numerical results revealed that the majority of the sand dunes were eroded by the first wave, especially during the strong return flow of the receding wave. Large flows and sand dune erosions can occur elsewhere if tsunamis inundate a plain with a limited shore-normal width. These events could cause large-scale morphological changes comparable to those that occurred in Rikuzentakata City.

Locality and nonlocality of electronic structures of molecular systems: Toward QM/MM and QM/QM approaches

We present a simple guideline to inspect the large molecular systems towards QM/MM theory and various types of divide-and-conquer electronic structure theories, in which we utilize on the linear-response function. We present the basic ideas of our approach, simple introduction of the computational method, and some numerical results.

Instability In Chemical Bonds: Uno Cascc, Resonating Ucc And Approximately Projected Ucc Methods To Quasi-Degenerate Electronic Systems

We review several versions of coupled-cluster (CC) methods based on spin-unrestricted Hartree–Fock (UHF) approximation. A multireference (MR) CC theory by the use of UHF natural orbitals (UNO), UNO CASCC, is revisited to elucidate scope and limitation of UHF coupled-cluster (CC) methods and two types of quantum corrections for UHF CC (UCC) solutions: first one is the approximate spin-projected UCC scheme (AP UCC) based on Heisenberg model Hamiltonian, and second one is the recently developed resonating UCC configuration interaction (Res-UCC CI) approach. In this article, we examine these CC-based approaches for quasi-degenerate electronic systems such as dissociation of covalent bonds. The computational results are discussed in comparison with those of the MR-CC theory. Our methods have been applied to exchange-coupled systems and ion-radical systems, which have been accepted current interests.

How to determine boundaries for QM/MM calculations: A guideline based on linear response function for glutathione

Quantum mechanics/molecular mechanics (QM/MM) methods have grown to be a standard tool for chemical reactions in biological systems. Still, the remaining problem is that the MM point charges induce artificial polarizations in QM regions, spoiling the quality of the QM calculations. Thus, how to determine boundaries between QM and MM regions is an essential issue for QM/MM calculations. Recently, we proposed the use of a linear response function as an indicator to examine the validity of the replacement of QM peripheral ligands with MM point charges. In this study, we examine the glutathione molecule, for which protonation models have been proposed so far. The calculated results are discussed in relation to the QM/MM modeling of this system.

Multireference Density Functional Study of Atomic and Molecular Magnetic Systems

We present the complete‐active‐space density functional theory (CAS‐DFT) approach for degenerate and nearly degenerate systems. In this method, we solve the effective CAS‐DFT equation in order that the Euler equation of CAS‐DFT is satisfied. The simple applications for atomic and molecular magnetic systems such as atomic multiplets, organic radicals, and Cu(II) acetate are presented. The results are discussed in relation to the theory of magnetism.

A parallel algorithm for generating molecular integrals over MO basis sets

Abstract In the post Hartree–Fock theories such as multi-configuration self consistent field and configuration interaction, two electron integral transformation to molecular orbital sets is the most time consuming process for large-scale calculations. Parallelization is key to minimize the computer time for it. Then, a parallel integral-driven algorithm is presented for the integral transformation.

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

A massively parallel program for quantum mechanical‐molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc‐pVDZ and B3LYP/cc‐pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6‐31G** calculations. We also performed excited QM/MM‐MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH‐insensitive and photo‐stable ultramarine fluorescent protein. Platypus accelerated on‐the‐fly excited‐state QM/MM‐MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50‐ps (200,000‐step) on‐the‐fly excited‐state QM/MM‐MD simulations for the SIRIUS in water.

A spin density version of linear response function: Toward guidelines of QM/MM boundaries for reliable computations

In this study, we developed the linear response function (LRF) approach for spin degree of freedom towards QM/MM boundary problem of spin-extended calculations. We examined a heme of a myoglobin to exemplify how to use our LRF approach.