Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Photoinduced magnetization of the cyano-bridged 3d-4f heterobimetallic assembly Nd(DMF)(4)(H(2)O)(3)(micro-CN)Fe(CN)(5).H(2)O (DMF = N,N-dimethylformamide)

Photoinduced magnetization of the cyano-bridged 3d-4f heterobimetallic assembly Nd(DMF)4(H2O)3(mu-CN)Fe(CN)5.H2O (1) (DMF = N,N-dimethylformamide) is described in this paper. The chiMT values are enhanced by about 45% after UV light illumination in the temperature range of 5-50 K. We propose that UV light illumination induces a structural distortion in 1. This small structural change is propagated by molecular interactions in the inorganic network. Furthermore, the cooperativity resulting from the molecular interaction functions to increase the activation energy of the relaxation processes, which makes observation of the photoexcited state possible. The flexible network structure through the hydrogen bonds in 1 plays an essential role for the photoinduced phenomenon. This finding may open up a new domain for developing the molecule-based magnetic materials.     

Enantioselective Morita–Baylis–Hillman reaction catalyzed by a chiral phosphine oxide

An application of a hypervalent silicon complex, generated from a chiral phosphine oxide catalyst and silicon tetrachloride, to the enantioselective organocatalytic Morita–Baylis–Hillman reaction is described. A chloride anion liberated from the hypervalent silicon complex smoothly generated a γ-chloro silyl enol ether that subsequently reacted with an aldehyde to afford the Baylis–Hillman adducts in good yields and with good enantioselectivities.     

Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method

Journal of Computer-Aided Molecular Design - Enhancer of zeste homolog 2 (EZH2) is a histone lysine methyltransferase that is overexpressed in many cancers. Numerous EZH2 inhibitors have been...     

Efficient direct electron transfer with enzyme on a nanostructured carbon film fabricated with a maskless top-down UV/ozone process

We have developed a new carbon film electrode material with thornlike surface nanostructures to realize efficient direct electron transfer (DET) with enzymes, which is very important for various enzyme biosensors and for anodes or cathodes used in biofuel cells. The nanostructures were fabricated using UV/ozone treatment without a mask, and the obtained nanostructures were typically 2-3.5 nm high as confirmed by atomic force microscopy measurements. X-ray photoelectron spectroscopy and transmission electron microscopy revealed that these nanostructures could be formed by employing significantly different etching rates depending on nanometer-order differences in the local sp(3) content of the nanocarbon film, which we fabricated with the electron cyclotron resonance sputtering method. These structures could not be realized using other carbon films such as boron-doped diamond, glassy carbon, pyrolyzed polymers based on spin-coated polyimide or vacuum-deposited phthalocyanine films, or diamond-like carbon films because those carbon films have relatively homogeneous structures or micrometer-order crystalline structures. With physically adsorbed bilirubin oxidase on the nanostructured carbon surface, the DET catalytic current amplification was 30 times greater than that obtained with the original carbon film with a flat surface. This efficient DET of an enzyme could not be achieved by changing the hydrophilicity of the flat carbon surface, suggesting that DET was accelerated by the formation of nanostructures with a hydrophilic surface. Efficient DET was also observed using cytochrome c.     

Structure of cyano-bridged Eu(III)—Co(III) bimetallic assembly and its application to photophysical verification of photomagnetic phenomenon

New crystal structure of Eu(DMF)₄(H₂O)₃Co(CN)₆·H₂O (DMF = N,N′-dimethylformamide) (Eu-Co) has been determined to be monoclinic, P2(1)/n, a = 19.796(12) Å, b = 8.862(11) Å, c = 17.525(10) Å, β = 96.26(5)°, V = 3056(5) ų, Z = 4. The Eu(III) ion adopts an antiprismatic eight-coordination and forms a cyano bridge with r(Eu-N) = 2.496(7) Å and Θ(Eu-N-C) = 165.7(7)° to the Co(III) ion. The complex exhibits some common features with the Eu-Fe complex. Diffuse reflectance electronic spectra and magnetic susceptibility of Eu-Cr, Eu-Mn, Eu-Fe, and Eu-Co complexes were compared. By substituting the metal ions, both electronic and structural features affected the charge transfer bands and superexchange interactions concerning cyanide ligands. In addition, only Eu-Co exhibited ⁵ D ₀ → ⁷ F ₂ and ⁵ D ₀ → ⁷ F ₁ luminescence bands at 16300 cm^?1 and 16900 cm^?1, respectively at 298 K (λ_ex = 360 nm (27000 cm^?1)), because quenching by cyano-bridged ions did not prevent Eu(III) ion from exhibiting emission. Thus, only Eu-Co may be suitable for verification of an assumption of mechanism concerning drastic photoinduced magnetic changes for Nd-Fe. Merely small decrease of magnetization was observed for Eu-Co after UV light irradiation at 2.0 K. This result was attributed to slight structural changes around cyano bridges without transitions of spin states.     

trans‐Bis(2,2‐diphenyl­ethyl­amine‐κN)bis­(5,5‐diphenyl­hydantoinato‐κN3)copper(II) and its chloro­form disolvate

The crystal structures of the title compounds, [Cu(C₁₅H₁₁N₂O₂)₂(C₁₄H₁₅N)₂] and [Cu(C₁₅H₁₁N₂O₂)₂(C₁₄H₁₅N)₂]·2CHCl₃, respectively, have been determined. The red disolvate complex affords a square‐planar CuN₄ coordination environment in which the Cu^II atom lies on a centre of symmetry. The blue solvent‐free complex affords a distorted square‐pyramidal CuN₄O coordination environment and adjacent mol­ecules form centrosymmetric dimers. A comparison of the different crystal structures focuses on the role of the solvent mol­ecules in supramolecular assemblies of the copper(II) complexes.     

Bis­(acetone‐κO)­bis(N,N′‐di­methyl­ethyl­enedi­amine‐κ2N,N′)copper(II) diperchlorate

The title compound, [Cu(C₄H₁₂N₂)₂(C₃H₆O)₂](ClO₄)₂, is the first structurally characterized Cu^II complex having acetone as axial ligands. The complex adopts an elongated octahedral trans‐[CuN₄O₂] coordination geometry, with the Cu atom having 222 site symmetry. The axial Cu—O(acetone) and in‐plane Cu—N bond lengths are 2.507 (5) and 2.041 (3) Å, respectively.     

Lariatins, antimycobacterial peptides produced by Rhodococcus sp. K01-B0171, have a lasso structure

Two antimycobacterial agents, lariatins A and B, were isolated from the culture broth of Rhodococcus sp. K01-B0171. Their structures were elucidated by spectral analysis and advanced protein chemical methods to be unique cyclic peptides, which consist of 18 and 20 L-amino acid residues with an internal linkage between the gamma-carboxyl group of Glu8 and the alpha-amino group of Gly1. The three-dimensional structure of lariatin A deduced from NMR data by dynamical simulated annealing method indicates that the tail segment (Trp9-Pro18) passes through the ring segment (Gly1-Glu8) to form a 'lasso' structure.