Effects of oligoDNA template length and sequence on binary self-assembly of a nucleotide bolaamphiphile

Templated self-assembly of nucleotide bolaamphiphile 1 (in which a 3'-phosphorylated thymidine moiety is connected to each end of a long oligomethylene chain) with a 10-, 20-, 30-, or 40-meric single-stranded oligoadenylic acid (2, 3, 4, or 5) led to the formation of right-handed helical nanofibers in 0.1x Tris/EDTA (TE) buffer solutions. The helical pitch increased as the length of the oligoadenylic acid template increased. DNA composed of oligoadenylic and oligocytidylic acid sequences (6, 7, and 8) also acted as templates to induce the formation of helical nanofiber structures. The diameter of the nanofibers remained constant (6-6.6 nm) irrespective of the template used. The binary self-assembly of 1 with 4 also produced higher-order, double-stranded nanofibers.     

Assessment of the efficiency of long-range corrected functionals for some properties of large compounds

Using the long-range correction (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated a series of properties that are known to be poorly reproduced by standard functionals: Bond length alternation of pi-conjugated polymers, polarizabilities of delocalized chains, and electronic spectra of extended dyes. For each of these properties, we present cases in which traditional hybrid functionals do provide accurate results and cases in which they fail to reproduce the correct trends. The quality of the results is assessed with regard to experimental values and/or data arising from electron-correlated wave function approaches. It turns out that (i) both LC-DFT and CAM-B3LYP provide an accurate bond length alternation for polyacetylene and polymethineimine, although for the latter they decrease slightly too rapidly with chain length. (ii) The LC generalized gradient approximation and MP2 polarizabilities of long polyphosphazene and polymethineimine oligomers agree almost perfectly. In the same way, CAM-B3LYP corrects the major part of the B3LYP faults. (iii) LC and CAM techniques do not help in correcting the nonrealistic evolution with chain length of the absorption wavelengths of cyanine derivatives. In addition, though both schemes significantly overestimate the ground to excited state transition energy of substituted anthraquinone dyes, they provide a more consistent picture once a statistical treatment is performed than do traditional hybrid functionals.     

First hyperpolarizability of polymethineimine with long-range corrected functionals

Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated the longitudinal dipole moments and static electronic first hyperpolarizabilities of increasingly long polymehtineimine oligomers. For comparison purposes Hartree-Fock (HF), Moller-Plesset perturbation theory (MP2), and conventional pure and hybrid functionals have been considered as well. HF, generalized gradient approximation (GGA), and conventional hybrids provide too large dipole moments for long oligomers, while LC-DFT allows to reduce the discrepancy with respect to MP2 by a factor of 3. For the first hyperpolarizability, the incorrect evolution with the chain length predicted by HF is strongly worsened by BLYP, Perdew-Burke-Ernzerhof (PBE), and also by B3LYP and PBE0. On the reverse, LC-BLYP and LC-PBE hyperpolarizabilities are correctly predicted to be positive (but for the two smallest chains). Indeed, for medium and long oligomers LC hyperpolarizabilities are slightly smaller than MP2 hyperpolarizabilities, as it should be. CAM-B3LYP also strongly improves the B3LYP results, though a bit less impressively for small chain lengths. The present study demonstrates the efficiency of long-range DFT, even in very pathological cases.     

Unambiguous Stereochemical Assignment of Cyclo(Phe-Pro), Cyclo(Leu-Pro), and Cyclo(Val-Pro) by Electronic Circular Dichroic Spectroscopy

2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).     

Origin of the X‐ray magnetic circular dichroism at the L‐edges of the rare‐earths in RxR1−x′Al2 systems

An X‐ray magnetic circular dichroism (XMCD) study performed at the rare‐earth L_2,3‐edges in the R_xR_1?x′Al₂ compounds is presented. It is shown that both R and R′ atoms contribute to the XMCD recorded at the L‐edges of the selected rare‐earth, either R or R′. The amplitude of the XMCD signal is not directly correlated to the magnetization or to the value of the individual (R, R′) magnetic moments, but it is related to the molecular field acting on the rare‐earth tuned in the photoabsorption process. This result closes a longstanding study of the origin of the XMCD at the L‐edge of the rare‐earths in multi‐component systems, allowing a full understanding of the exact nature of these signals.     

静止水中单个上升气泡的直接数值模拟

本文发展了基于Front Tracking的直接数值模拟方法研究气液两相界面的迁移特性,该方法对气液两相采用半隐式的分步法直接求解N-S方程,耦合Front Tracking Method获得两相界面的三维变形。针对无边界以及垂直壁面附近静止水中的单个气泡上升过程进行模拟,研究气泡运动的机理以及气泡与壁面的相互作用。数值模拟准确再现了气泡的上升过程和变形,不同Re数下气泡的上升速度计算结果同经验关联式非常吻合,验证了该方法的有效性。随后分析了气泡周围流场的结构,发现壁面对气泡周围流场的抑制是壁面对气泡作用力的主要原因,将导致气泡逐渐偏离垂直壁面。     

Structural and spectroscopic characterization of a diruthenium o-dioxolene complex possessing a singly occupied molecular orbital delocalized over the entire molecule, [Ru2(3,6-DTBDiox)4]-

Chemical oxidation of [Ru2(6+)(3,6-DTBCat)4]2- affords [n-Bu4N][Ru2(3,6-DTBDiox)4].acetone (2.acetone). The oxidized species was characterized by X-ray crystallographic analysis and EPR, and the delocalization of the unpaired electron over the entire molecule was indicated. This example showed that the utilization of redox-active ligands into a Ru2 complex expanded the degree of freedom in the electronic structure. DFT calculations support this view, and the spin population was estimated to be approximately 18% and 82% for the Ru2 core and the four dioxolene ligands, respectively.     

Application of a conproportionation reaction to a synthesis of shape-controlled gold nanoparticles

Synthesis of gold nanoparticles with multiple shapes by a modified seeding growth method is reported. The optical extinction spectra of a mixture of the seed and growth solutions indicate that the seed particle size decreases during stirring the mixture by a conproportionation reaction of Au metal with Au(III) ions. This conproportionation reaction is used to investigate the effects of variation in seed particle size on the resultant gold nanoparticle shape. When single crystalline and multiply twinned particles are used as the seed particles, they grow into gold nanorods and nanobipyramids, respectively. By letting the seed particles experience the conproportionation reaction before the particle growth to decrease the size, the surface of resultant nanoparticles roughens. Increasing the conproportionation reaction time up to 5 min, multi-branched gold nanoparticles with many lattice defects grow from both of the seed particles. This indicates that the conproportionation reaction is useful to generate lattice defects during the particle growth, which lead to the formation of gold nanoparticles with complex shapes.