Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.     

Mechanically activated rupture of single covalent bonds: evidence of force induced bond hydrolysis

We have used temperature-dependent single molecule force spectroscopy to stretch covalently anchored carboxymethylated amylose (CMA) polymers attached to an amino-functionalized AFM cantilever. Using an Arrhenius kinetics model based on a Morse potential as a one-dimensional representation of covalent bonds, we have extracted kinetic and structural parameters of the bond rupture process. With 35.5 kJ mol(-1), we found a significantly smaller dissociation energy and with 9.0 × 10(2) s(-1) to 3.6 × 10(3) s(-1) also smaller Arrhenius pre-factors than expected for homolytic bond scission. One possible explanation for the severely reduced dissociation energy and Arrhenius pre-factors is the mechanically activated hydrolysis of covalent bonds. Both the carboxylic acid amide and the siloxane bond in the amino-silane surface linker are in principle prone to bond hydrolysis. Scattering, slope and curvature of the scattered data plots indicate that in fact two competing rupture mechanisms are observed.     

Chromophores in cellulosics, VI. First isolation and identification of residual chromophores from aged cotton linters

In the present work, aged cotton linters have been analyzed for their chromophore content according to the CRI (“chromophore release & identification”) method. Despite the very low contents in the ppb range, nine chromophores have been unambiguously identified, which makes this account the first one on defined chromophoric structures isolated from cotton. A common feature of the chromophores are 2-hydroxy-[1,4]benzoquinone, 2-hydroxyacetophenone and 5,8-dihydroxynaphthoquinone moieties, which resemble chromophoric structures found in other cellulosic substrates, such as bleached pulps or fibers. The finding of these compounds in lignin-free cotton linters confirms the previous hypothesis that those chromophores are formed from (oxidized) carbohydrate structures rather than from lignin fragments.     

Hydroxyl orientations in cellobiose and other polyhydroxyl compounds: modeling versus experiment

Theoretical and experimental gas-phase studies of carbohydrates show that their hydroxyl groups are located in homodromic partial rings that resemble cooperative hydrogen bonds, albeit with long H…O distances and small O–H…O angles. On the other hand, anecdotal experience with disaccharide crystal structures suggested that these clockwise ‘c’ or counter-clockwise (reverse ‘r’) sequences are not prevalent in the crystalline state. The situation was clarified with quantum mechanics calculations in vacuum and in continuum solvation, as well as Atoms-In-Molecules analyses. From the experimental side, the Cambridge Structural Database was searched. Geometric criteria for these sequences were developed. A criterion based on 120° ranges of hydroxyl orientations accepted 4% of sequences as having ‘c,c’ or ‘r,r’ orientations instead of the 7% expected based on chance. Criteria based on an O–H…O angle > 90° and a 90° lower limit of the absolute value of the H–O–C…H improper torsion accepted 7.0% of the 358 sequences as ‘c,c’ or ‘r,r’. Highly variable orientation of the hydroxyl groups in crystals was seen to depend mostly on strong inter-residue or intermolecular hydrogen bonds. That lack of specific orientation in general for the crystal structures was supported by the solvated calculations that showed very little variation in the energy when one of the hydroxyl groups in 1,2-dihydroxycyclohexane was rotated. The vacuum calculations found the energy to vary with rotation by more than 4 kcal/mol, confirming the gas-phase experiments and calculations on more complicated molecules. Molecules examined in some detail include scyllo inositol and native and methylated cellobiose.     

Design of stable polyether-magnetite complexes in aqueous media: effects of the anchor group, molecular weight, and chain density

The colloidal stability of polymer-stabilized nanoparticles is critical for therapeutic use. However, phosphates in physiological media can induce polymer desorption and consequently flocculation. Colloidal characteristics of PEO-magnetite nanoparticles with different anchors for attaching PEO to magnetite were examined in PBS. The effects of the number of anchors, PEO molecular weight, and chain density were examined. It was observed that ammonium phosphonates anchored PEO to magnetite effectively in phosphate-containing solutions because of interactions between the phosphonates and magnetite. Additionally, a method to estimate the magnetite surface coverage was developed and was found to be critical to the prediction of colloidal stability. This is key to understanding how functionalized surfaces interact with their environment.     

Molecular dynamics extended for fluctuating networks: Application to water

Molecular simulation models are increasingly important tools in efforts to understand the role that water plays in biochemical processes. However, existing models of water have limited capacity to deal with the characteristics of hydrogen bond networks. This article proposes a new fluctuating network (FN) algorithm as an extension of the standard molecular dynamics algorithm. The new algorithm allows for the simulation of a molecular system based on an underlying network, such as the hydrogen bond network in water. This algorithm distinguishes strong from weak network connections, applying a potential that best describes the specific connection behavior. We model liquid water with this new technique using a single‐site, isotropic, short‐range potential. We successfully reproduce liquid water's signature molecular spacing (as represented by the radial distribution function) and characterize its dynamic properties including the exponential hydrogen bond lifetime distribution, diffusion rate, and average hydrogen bonds per molecule. The FN algorithm allows exploration of the behavior of networked systems where explicit coordination limits are required. As such it could also be used to model covalent interactions, reaction dynamics, and applied to simulation of cellular networks. © 2012 Wiley Periodicals, Inc.     

Biosupramolecular nanowires from chlorophyll dyes with exceptional charge-transport properties

Conductive tubes: Self-assembled nanotubes of a bacteriochlorophyll derivative are reminiscent of natural chlorosomal light-harvesting assemblies. After deposition on a substrate that consists of a non-conductive silicon oxide surface (see picture, brown) and contacting the chlorin nanowires to a conductive polymer (yellow), they show exceptional charge-transport properties.     

One stone kills four birds: a novel diazaperinone 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one recognizes four different metal ions

A novel diazaperinone 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one has been successfully synthesized through a one-step condensation. Single crystal X-ray analysis shows that the product is of planar structure with strong π?π interactions and H-bonding. Interestingly, the 12H-pyrazino[2′,3′:3,4]pyrrolo[1,2-a]perimidin-12-one can recognize three different metal cations Cu²⁺, Ag⁺ and Hg²⁺ via naked eye visualization, and shows turn-on fluorescence for Fe³⁺ and Ag⁺ among the 22 metal cations.     

β-Technetium trichloride: formation, structure, and first-principles calculations

A second polymorph of technetium trichloride, β-TcCl(3), has been identified from the reaction between Tc metal and Cl(2) gas. The structure of β-TcCl(3) consists of infinite layers of edge-sharing octahedra, similar to its MoCl(3) and RuCl(3) analogues. The Tc-Tc distance [2.861(3) ?] between adjacent octahedra is indicative of metal-metal bonding. Earlier theoretical work predicted that β-TcCl(3) is less stable than α-TcCl(3). In agreement with the prediction, β-TcCl(3) slowly transforms into α-TcCl(3) (Tc(3)Cl(9)) over 16 days at 280 °C.     

Zur Struktur der Tetrahydro-4-phenylspiro([1]benzopyran-2,4′(1′H)-pyrimidin)-2′(3′H)-one bzw.-thione Über Heterocyclen, 49. Mitt

The structures of tetrahydro-4-phenylspiro([1]benzopyran-2,4(1H)-pyrimidin)-2(3H)-ones and-thiones4 a, b resp., are proved by synthesis. 3-(2-methoxy-3,5-dimethylphenyl)-3-phenylpropionic acid11 b is prepared from 3,4-dihydro-6,8-dimethyl-4-phenylcoumarin10. The lithium salt of11 b reacts with isobutenyl-lithium to 1-(2-methoxy-3,5-dimethylphenyl)-5-methyl-1-phenyl-4-hexen-3-on12 a. 12 a is transferred with urea in acid medium and NH₄CNS resp. in a mixture of dihydro-6-[2-(2-methoxy-3,5-dimethylphenyl)-2-phenyläthyl]-4,4-dimethyl-2(1H)-pyrimidinone and-thione13 a, b and tetrahydro-6-[2-(2-methoxy-3,5-dimethylphenyl)-2-phenyläthyliden]-4,4-dimethyl-2(1H)-pyrimidinone and-thione14 a, b resp.14 b leads to13 a, b with H₂O₂. Heating of13 a, 14 a and14 b resp. with pyridin-HCl leads to the spiro compounds4 a, b.