A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates

We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer centroids in the imaginary-time path integral theory. This novel kind of reaction coordinate, which may be called the "centroid IRC," corresponds to the minimum free energy path connecting reactant and product states with a least amount of reversible work applied to the center of masses of the quantum nuclei, i.e., the centroids. We provide a numerical procedure to obtain the centroid IRC based on first principles by combining ab initio path integral simulation with the string method. This approach is applied to NH(3) molecule and N(2)H(5) (-) ion as well as their deuterated isotopomers to study the importance of nuclear quantum effects in the intramolecular and intermolecular proton transfer reactions. We find that, in the intramolecular proton transfer (inversion) of NH(3), the free energy barrier for the centroid variables decreases with an amount of about 20% compared to the classical one at the room temperature. In the intermolecular proton transfer of N(2)H(5) (-), the centroid IRC is largely deviated from the "classical" IRC, and the free energy barrier is reduced by the quantum effects even more drastically.     

57Fe M?ssbauer analysis of the Upper Triassic-Lower Jurassic deep-sea chert: Paleo-redox history across the Triassic-Jurassic boundary and the Toarcian oceanic anoxic event

We investigated the paleo-redox change across the Triassic-Jurassic (T-J) boundary (～200?Ma) and the Early Toarcian oceanic anoxic event (T-OAE; ～183?Ma) recorded in the Upper Triassic to Lower Jurassic pelagic deep-sea cherts in the Inuyama area, Central Japan. The present ⁵⁷Fe M?ssbauer spectroscopic analysis for these cherts identified five iron species, i.e., hematite (α-Fe₂O₃), pyrite (FeS₂), paramagnetic Fe^3?+?, and two paramagnetic Fe^2?+? with different quadrupole splittings. The occurrence of hematite and pyrite in deep-sea cherts essentially indicates primary oxidizing and reducing depositional conditions, respectively. The results confirmed that oxidizing conditions persisted in deep-sea across the T-J boundary. In contrast, across the T-OAE, deep-sea environment shifted to reducing conditions. The first appearance of the gray pyrite-bearing chert marked the onset of the deep-sea oxygen-depletion in the middle Pliensbachian, i.e., clearly before the shallow-sea T-OAE.     

A Small Molecule Affecting the Replication of Trinucleotide Repeat d(GAA)n

A newly designed ligand, methylcarbamoylnaphthyridine dimer (MCND), was synthesized and characterized. Ligand binding to d(GAA)₁₀ was investigated by UV thermal denaturation, circular dichroism spectroscopy, surface plasmon resonance, and cold‐spray‐ionization time‐of‐flight mass spectrometry. The results indicated that MCND bound to the d(GAA)_n repeat to form a stable hairpin structure with a major binding stoichiometry of 3:1. The most likely binding site was identified as the G? G mismatch in the AGA/AGA triad. The polymerase stop assay showed that MCND binding to the d(GAA)_n repeat effectively interfered with the extension of the primer at the first two GAA sites on the template with both prokaryotic Taq DNA polymerase and human DNA polymerase α.     

Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H2O)4 on a semiempirical potential energy surface

Path-integral molecular dynamics simulations for the HCl(H₂O)₄ cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H₂O)₄ cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.     

Dislocation interaction with radiation-induced single halogen interstitials in KBr

Mechanism of radiation hardening by single halogen interstitials has been studied in KBr. It is found that the interstitial ions more strongly interrupt dislocation movements than the atoms do. The I_A center-dislocation interaction involves thermal activation. The maximum force in the interaction process is obtained to be 1.6 x 10^-4 dyne. The results of linear elastic calculations suggest that this interaction is elastic in nature.     

Syntheses, Characterization, and Molecular Mechanics Calculations of Optically Active Silatrane Derivatives

A series of optically active silatrane derivatives, [Si{N(CHRCH(2)O)(CH(2)CH(2)O)(2)}X] (R = Me, i-Pr; X = Ph, OMe) has been synthesized by the reaction of optically active triethanolamine derivatives with XSi(OMe)(3), and characterized by (1)H NMR, (13)C NMR, (29)Si NMR, and mass spectroscopy, and the structures of six compounds have been determined by X-ray analysis. Molecular mechanics methods have also been employed to obtain the energy-minimized structures. The (29)Si NMR chemical shifts and the lengths of Si-N determined by X-ray analysis are sensitive to the bulkiness of the substituent (R). The Si-X bond lengths (X: trans position to nitrogen) do not appreciably differ from one another. The MM2 calculations indicated that the substituent exists in the equatorial position, and the results are in agreement with those of X-ray analysis and (1)H NMR spectroscopy. Crystallographic data: [R = H; X = OMe], C(7)H(15)NO(4)Si, orthorhombic, Pna2(1), a = 13.407(1) ?, b = 8.761(2) ?, c = 8.191(1) ?, Z = 4; [R = Me; X = OMe], C(8)H(17)NO(4)Si, orthorhombic, P2(1)2(1)2(1), a = 10.110(3) ?, b = 11.083(2) ?, c = 9.474(2) ?, Z = 4; [R = i-Pr; X = OMe], C(10)H(21)NO(4)Si, monoclinic, P2(1), a = 8.481(1) ?, b = 7.805(1) ?, c = 10.218(2) ?, beta = 111.31(1) degrees, Z = 2; [R = Me; X = Ph], C(13)H(19)NO(3)Si, orthorhombic, P2(1)2(1)2(1), a = 8.813(1) ?, b = 11.137(2) ?, c = 13.757(1) ?, Z = 4; [R = i-Pr; X = Ph], C(15)H(23)NO(3)Si, orthorhombic, P2(1)2(1)2(1), a = 8.365(1) ?, b = 13.538(2) ?, c = 13.841(2) ?, Z = 4.     

Activated carbon membrane for water treatments: Application to decolorization of coke furnace wastewater

An activated carbon membrane to be used in water treatments was developed and the decolorization of the coke furnace wastewater was successfully demonstrated as a model case. The activated carbon membrane was prepared by carbonizing poly-vinydenchloride (PVdC) and poly-vinylalcohol (PVA) microspheres aggregating on and within a ceramic pipe. The membrane developed in this work was suspected to have a bidispersed structure, which made it possible to play the roles of both a porous membrane having the molecular weight cut-off of about 10,000 and an activated carbon bed where the dissolved organics with low molecular weight could be adsorbed. The activated carbon membrane developed in this work appears to be useful for compact water treatment processes.     

Probing the shape and stereochemistry of molecular orbitals in locally flexible aromatic chains: a penning ionization electron spectroscopy and Green's function study of the electronic structure of biphenyl

We report on the results of an exhaustive study of the interplay between the valence electronic structure, the topology and reactivity of orbitals, and the molecular structure of biphenyl by means of Penning ionization electron spectroscopy in the gas phase upon collision with metastable He*(2(3)S) atoms. The measurements are compared with one-particle Green's function calculations of one-electron and shake-up valence ionization spectra employing the third-order algebraic diagrammatic construction scheme [ADC(3)]. Penning ionization intensities are also analyzed by means of the exterior electron-density model and comparison with photoelectron spectra: in contrast with the lines originating from sigma orbitals, ionization lines belonging to the pi-band system have large Penning ionization cross sections due to their greater extent outside the molecular van der Waals surface. The involved chemi-ionization processes are further experimentally investigated using collision-energy-resolved Penning ionization electron spectroscopy. The cross sections of pi-ionization bands exhibit a markedly negative collision-energy dependence and indicate that the interaction potential that prevails between the molecule and the He*(2(3)S) atom is strongly attractive in the pi-orbital region. On the other hand, the partial ionization cross sections pertaining to sigma-ionization channels are characterized by more limited collision-energy dependencies, as a consequence of rather repulsive interactions within the sigma-orbital region. A comparison of ADC(3) simulations with the Penning ionization electron spectra and UV photoelectron spectra measured by Kubota et al. [Chem. Phys. Lett. 1980, 74, 409] on thin films of biphenyl deposited at 170 and 109 K on copper demonstrates that biphenyl molecules lying at the surface of polycrystalline layers adopt predominantly a planar configuration, whereas within an amorphous sample most molecules have twisted structures similar to those prevailing in the gas phase.     

Stepwise molding of a highly selective ribonucleopeptide receptor

The structural characteristics of RNA-peptide (RNP) complexes are suitable for molding of a ligand-binding pocket of the RNP complex in a stepwise manner. The first step involves molding of the RNA subunit by in vitro selection of an RNP pool originating from an RNA library and the peptide, as previously reported for the construction of an ATP-binding RNP complex from an RRE RNA-Rev peptide complex. The second step involves selection from an RNP library consisting of Rev peptides with randomized amino acid residues and the RNA subunit selected in the first molding. The ATP-binding pocket produced by sequential molding of RNA and peptide subunits shows higher affinity to ATP and a distinct specificity for ATP versus dATP as compared to the ATP-binding RNP receptor in which only the RNA subunit has been molded. The second step selection from the peptide-based RNP library allows expansion of the ATP recognition surface, consisting of both RNA and peptide subunits, to enhance the affinity and selectivity to discriminate ATP against dATP. Our approach of stepwise molding offers the advantage of increasing the diversity of the RNP library by utilizing characteristics of different biopolymers. The ribonucleopeptide-based, multi-subunit approach is also extendable to other biomacromolecular assemblies, which may yield artificial receptors and enzymes with increased specificity and more diverse chemical activities.