Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle

We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical cutoff distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications.     

Critical behavior of megabase-size DNA toward the transition into a compact state

We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.     

Photophysical properties and photochemistry of EE-, EZ-, and ZZ-1,4-dimethoxy-2,5-bis[2-(thien-2-yl)ethenyl] benzene in solution: theory and experiment

Photophysical properties and photoisomerization of 1,4-dimethoxy-2,5-bis[2-(thien-2-yl)ethenyl] benzene (DMTB) have been investigated for the EE-, EZ-, and ZZ- stereoisomers. The EE-DMTB was prepared, and the absorption/fluorescence spectra of EE- isomer as well as transient spectra in photoisomerization among three isomers were observed. Absorption and fluorescence spectra of three isomers were analyzed by the symmetry-adapted cluster-configuration interaction (SAC-CI) and time-dependent density functional theory (TDDFT) methods. The characteristics of the absorption spectra of three isomers were satisfactorily reproduced by the direct SAC-CI and TDDFT methods in both peak position and intensity. The relative stability of three isomers and the photoisomerization among these isomers were also examined theoretically. The ground (S(0)) and first excited state (S(1)) geometries were calculated by the DFT/TDDFT method with the M06HF functional, and the calculated S(0) structures of EE- and ZZ- isomers agreed well with those of the X-ray structures. The geometry relaxation in the S(1) state was interpreted with regard to the excitation character. The solvent effect in the absorption and fluorescence spectra was examined by the polarizable continuum model (PCM) and was found to be 0.05-0.20 eV, reflecting the charge polarization. The results show that the photophysical properties of DMTB can be controlled with the conformation constraint and also indicate the possibility of a photofunctional molecular device such as a switching function.     

Proton transfers along hydrogen bonds in the tautomerization of purine

Tautomerization of purine in the water cluster was investigated by the use of DFT calculations. The correlation between the reaction paths and the number of water molecules (n) was examined. For n = 3 and n = 4, concerted reaction paths were obtained. However, for n = 5, a stepwise path including an ion pair intermediate was found with small activation energies. The n = 4 + 3 and n = 4 + 3 + 9 models were calculated to give further small activation energies, where n = 4 constitutes the reaction center and +3 and +3 + 9 denote the number of catalytic water molecules. The combination of the in-plane deprotonation at the N9 site and the out-of-plane protonation at the N7 site makes the n = 4 model probable. Three protonated n = 4 + 3 + 9 routes, a, b, and c, composed of purineH(+)(H(2)O)(4+3+9) were investigated. The n = 4 + 3 moiety is also included in the three routes, and the route c (with the N1 protonation) was found to be most favorable. The purine tautomerization was found to involve the Zundel cation in the ion pair intermediate.     

Hyperstoichiometric interaction between silver and mercury at the nanoscale

Breaking through the stoichiometry barrier: as the diameter of silver particles is decreased below a critical size of 32 nm, the molar ratio of aqueous Hg(II) to Ag(0) drastically increases beyond the conventional Hg/Ag ratio of 0.5:1, leading to hyperstoichiometry with a maximum ratio of 1.125:1. Therein, around 99% of the initial silver is retained to rapidly form a solid amalgam with reduced mercury.     

Strategies for ensuring that regenerative cardiomyocytes function properly and in cooperation with the host myocardium

In developed countries, in which people have nutrient-rich diets, convenient environments, and access to numerous medications, the disease paradigm has changed. Nowadays, heart failure is one of the major causes of death. In spite of this, the therapeutic efficacies of medications are generally unsatisfactory. Although whole heart transplantation is ideal for younger patients with heart failure, many patients are deemed to be unsuitable for this type of surgery due to complications and/or age. The need for therapeutic alternatives to heart transplantation is great. Regenerative therapy is a strong option. For this purpose, several cell sources have been investigated, including intrinsic adult stem or progenitor cells and extrinsic pluripotent stem cells. Most intrinsic stem cells seem to contribute to a regenerative environment via paracrine factors and/or angiogenesis, whereas extrinsic pluripotent stem cells are unlimited sources of cardiomyocytes. In this review, we summarize the various strategies for using regenerative cardiomyocytes including our recent progressions: non-genetic approaches for the purification of cardiomyocytes and efficient transplantation. We expect that use of intrinsic and extrinsic stem cells in combination will enhance therapeutic effectiveness.     

Practical synthesis of (E)- and (Z)-2-silyl-3-penten-1-ols with high enantiopurity

Practical methods for the synthesis of the optically active (E)- and (Z)-2-silyl-3-pentene-1-ols are described. The optically pure (E)-allylsilane was synthesized from commercially available (R)-3-butyn-2-ol in five steps involving hydrozirconation followed by alkylation of the resulting alkenylmetal with BnOCH₂Cl. On the other hand, both enantiomers of the corresponding (Z)-allylsilane were prepared from commercially available dimethylphenylvinylsilane through epoxidation, the regioselective epoxide-opening reaction with 1-propynylmagnesium bromide, and the subsequent optical resolution using a lipase.     

Ammonothermal epitaxy of wurtzite GaN using an NH4I mineralizer

Purely wurtzite phase needle crystals and epitaxial layers of GaN were grown by the ammonothermal method using an NH₄I mineralizer. The inclusion of zincblende phase GaN was effectively eliminated by increasing the growth temperature higher than 500 °C. Accordingly, an approximately 20-μm-thick GaN epitaxial layer was achieved on the Ga-polar face of a c-plane GaN seed wafer at 520 °C. Although the characteristic deep state emission band dominated the room temperature photoluminescence spectrum, the near-band-edge emission of GaN was observed for both the needle crystals and the epitaxial layers. These results encourage one to grow better quality GaN crystals at a high growth rate under high-temperature growth conditions.     

Three-Body ΛNN → nNN Nonmesonic Weak Decay Process of Λ Hypernuclei

The fundamental motivation to study the non-mesonic weak decay (NMWD) of Λ hypernuclei is that it provides the unique channel for the information of the baryon–baryon weak interaction in SU3 _f group. The relative strength of the two main channels of NMWD whose decay processes are the Λp → np and Λn → nn has been the long standing puzzle during last several decades. The puzzling status has been settled down recently with the Γ _n / Γ _p value converging to ${\sim 0.5}$ . The large experimental values of Γ _n / Γ _p of the previous measurements turned out to be due to the surprisingly large contribution of the competing three-body NMWD, ΛNN → nNN process. This paper discusses about the first measurement of the branching ratio of the three-body NMWD process and the renormalized intra-nuclear cascade method adopted to disentangle the contribution of the three-body process out of those due to final state interaction. And the prospects of the more accurate measurement of the three-body process also are presented.     

Soluble-insoluble-soluble transitions of aqueous poly(N-vinylacetamide-co-acrylic acid) solutions

Several poly(N-vinylacetamide-co-acrylic acid)s with various copolymer compositions have been synthesized, and their unique phase-transition behavior in aqueous salt (Na2SO4 or NaCl) solutions was investigated. Copolymers containing more than 51 mol % N-vinylacetamide (NVA) show reentrant soluble-insoluble-soluble transitions with increasing temperature. The soluble-insoluble transition temperature (T(p1)) increased linearly with increasing NVA content, whereas the insoluble-soluble transition temperature (T(p2)) was almost constant irrespective of the NVA content. Potentiometric titration of the copolymer solutions suggested that the acrylic acid (AA) carboxyl groups form hydrogen bonds with the NVA amide groups even under soluble conditions. Dehydration of the NVA amides and their consequent hydrogen bonding with the AA carboxyl groups during the soluble-insoluble transition process was indicated by FTIR measurements. Addition of salt (Na2SO4 or NaCl) to the aqueous media reduces the solvent quality and enhances the intra- and interchain interactions of the copolymers. Thus, T(p1) was observed to decrease and T(p2) was observed to increase with increasing salt concentration. However, the addition of urea to the media reverses the concentration dependence of T(p1) and T(p2) by disturbing the intra- and interchain interactions of the copolymers.