Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order M?ller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.     

Coherent control protocol for separating energy-transfer pathways in photosynthetic complexes by chiral multidimensional signals

Adaptive optimizations performed using a genetic algorithm are employed to construct optimal laser pulse configurations that separate spectroscopic features associated with the two main energy-transfer pathways in the third-order nonlinear optical response simulated for the Fenna-Matthews-Olson (FMO) photosynthetic complex from the green sulfur bacterium Chlorobium tepidum. Superpositions of chirality-induced tensor components in both collinear and noncollinear pulse configurations are analyzed. The optimal signals obtained by manipulating the ratios of various 2D spectral peaks reveal detailed information about the excitation dynamics.     

Preparation of η2-complexes of fullerenes by reduction. Crystal structure and optical properties of {Ni(dppp)·(η2-C70)}·(C6H4Cl2)0.5

The new reduction method for preparation of η(2)-complexes of fullerenes with nickel-1,3-bis(diphenylphosphino)propane has been developed in which Ni(dppp)Cl(2) and C(60)(C(70)) mixtures are reduced with sodium tetraphenylborate. Single crystals of the first η(2)-complex of nickel with fullerene C(70): {Ni(dppp)·(η(2)-C(70))}·(C(6)H(4)Cl(2))(0.5) (1) (C(6)H(4)Cl(2) = o-dichlorobenzene) have been obtained as well as the previously described complex with fullerene C(60): {Ni(dppp)·(η(2)-C(60))}·(Solvent) (2). The crystal structure of 1 has been solved to show the coordination of nickel to the C-C bond of C(70) at the 6-6 ring junction of η(2)-type to form Ni-C(C(70)) bonds of 1.929-1.941(2) ? length, the shortest M-C bonds among those known for η(2)-complexes of fullerenes C(60) and C(70). The length of the C-C bond to which Ni atom is coordinated (1.494(3) ?) is noticeably longer than the average length of these bonds in C(70) (1.381(2) ?). Optical spectra of 1 in the IR- and UV-visible ranges have been analyzed to show the splitting of some C(70) bands due to C(70) symmetry lowering. The complex has a red-brown color in solution and manifests three bands in the visible range at 379, 467 and 680 nm. The solution of 1 is air sensitive since air exposure restores the color and absorption bands of the starting C(70) at 383 and 474 nm.     

On the geometry of spaces of oriented geodesics

Let M be either a simply connected pseudo-Riemannian space of constant curvature or a rank one Riemannian symmetric space, and consider the space L(M) of oriented geodesics of M. The space L(M) is a smooth homogeneous manifold and in this paper we describe all invariant symplectic structures, (para)complex structures, pseudo-Riemannian metrics and (para)Kähler structure on L(M).     

A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin

The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO∕EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 A? are investigated by performing FMO∕EFP geometry optimizations at the RHF∕cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF∕EFP are compared to those from the conventional RHF∕EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order M?ller-Plesset theory (MP2)∕cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure.     

Transformation of ionic liquid into carbon nanotubes in confined nanospace

We have developed a two-step filling process for the nano-reaction of ionic liquid in a tip-closed SWNT, where fullerenes are inserted at the end of the host SWNT as a plug to prevent the leakage of the confined ionic liquid during heat treatment.     

Engineering of a redox protein for DNA-directed assembly

Engineered enzyme conjugate of the small laccase enzyme from Streptomyces coelicolor and zinc finger DNA binding domain from Zif268 is demonstrated to bind double stranded DNA in a site specific manner while retaining enzymatic activity.     

Three-dimensional imaging of sulfides in silicate rocks at submicron resolution with multiphoton microscopy

We report the first application of multiphoton microscopy (MPM) to generate three-dimensional (3D) images of natural minerals (micron-sized sulfides) in thick (～120 μm) rock sections. First, reflection mode (RM) using confocal laser scanning microscopy (CLSM), combined with differential interference contrast (DIC), was tested on polished sections. Second, two-photon fluorescence (TPF) and second harmonic signal (SHG) images were generated using a femtosecond-laser on the same rock section without impregnation by a fluorescent dye. CSLM results show that the silicate matrix is revealed with DIC and RM, while sulfides can be imaged in 3D at low resolution by RM. Sulfides yield strong autofluorescence from 392 to 715 nm with TPF, while SHG is only produced by the embedding medium. Simultaneous recording of TPF and SHG images enables efficient discrimination between different components of silicate rocks. Image stacks obtained with MPM enable complete reconstruction of the 3D structure of a rock slice and of sulfide morphology at submicron resolution, which has not been previously reported for 3D imaging of minerals. Our work suggests that MPM is a highly efficient tool for 3D studies of microstructures and morphologies of minerals in silicate rocks, which may find other applications in geosciences.     

Temperature dependence of crystal growth of hexagonal ice (I(h))

The transformations between water and ice have many implications across numerous fields of study. A better understanding of this process would benefit many areas of science and technology such as medicine, biology, and atmospheric and material sciences. In the present work the temperature dependence of the rate of growth (melting) of the basal face of hexagonal ice I(h) and the effect of system size are investigated in molecular dynamics simulations. Using an effective pair potential model of water, systems are studied over temperatures ranging from T(M) - 40 to T(M) + 16 K, where T(M) is the melting temperature of the model. It is found that the growth rates reach a maximum value of 0.7 ? ns(-1) (7 cm s(-1)) at about 12 K below the melting temperature. A noticeable effect of the system size on the melting temperature and ice growth rates is observed; it is shown that the size effect arises in smaller systems due to the artificial ordering under periodic conditions. The decrease in melting entropy in the smallest system by 0.4 J (mol K)(-1) relative to the largest system results in an up-shift in the melting temperature by about 2 K. An almost 60% increase in the maximum growth rate is observed for the smallest system.