Investigation of lignin models of the biphenyl type by X-ray crystallography and NMR spectroscopy

Lignin models of the biphenyl type have been synthesized and crystal structures of two of them have been determined. The tetraacetate of 5,5-bis(hydroxymethyl)-3,3-dimethoxy-2,2-biphenyldiol crystallizes in space group witha=11.319(2),b=12.232(6),c=9.242(3) Å, =101.66(3)°, =108.14(2)°, =79.08(2)° andZ=2.R=0.036 (2720 observed [I>3(I)] reflections). The acetate of 5,5-di-tert-butyl-2,3,3-trimethoxy-2-biphenylol crystallizes in space group witha=11.972(2),b=21.621(3),c=9.834(1) Å, =91.18(1)°, =113.13(1)°. =98.42(1)°, andZ=4.R=0.050 (8129 observed [I>3(I)] reflections).¹H NMR and¹³C NMR data for the above-mentioned compounds and a third model, the diacetate of 5,5-bis(1-hydroxyethyl)-2,2,3,3-tetramethoxybiphenyl, are reported. Observed signal positions are compared with those calculated on the basis of crystal structure data. The possibilities to obtain structural information about biphenyl structures in lignins from NMR spectra are discussed.     

Novel tricyclic diamines 1. Synthesis of 1,4-diazaisotwistane and 1,4-diazahomoisotwistane as constrained 3-aminoquinuclidine isosteres

Synthesis of the novel tricyclic diamines 1,4-diazaisotwistane and 1,4-diazahomoisotwistane are described. These compact tricyclic cores have one tertiary and one secondary amine and may serve as ring-constrained isosteres of 3-aminoquinuclidine. Both tricycles were prepared by a similar strategy involving saturation of an appropriately substituted aromatic azaindole, functionalization and intramolecular alkylation.     

Observation of high soft x-ray drive in large-scale hohlraums at the National Ignition Facility

The first soft x-ray radiation flux measurements from hohlraums using both a 96 and a 192 beam configuration at the National Ignition Facility have shown high x-ray conversion efficiencies of ～85%-90%. These experiments employed gold vacuum hohlraums, 6.4 mm long and 3.55 mm in diameter, heated with laser energies between 150-635 kJ. The hohlraums reached radiation temperatures of up to 340 eV. These hohlraums for the first time reached coronal plasma conditions sufficient for two-electron processes and coronal heat conduction to be important for determining the radiation drive.     

Discrete data assimilation in the Lorenz and 2D Navier-Stokes equations

Consider a continuous dynamical system for which partial information about its current state is observed at a sequence of discrete times. Discrete data assimilation inserts these observational measurements of the reference dynamical system into an approximate solution by means of an impulsive forcing. In this way the approximating solution is coupled to the reference solution at a discrete sequence of points in time. This paper studies discrete data assimilation for the Lorenz equations and the incompressible two-dimensional Navier-Stokes equations. In both cases we obtain bounds on the time interval h between subsequent observations which guarantee the convergence of the approximating solution obtained by discrete data assimilation to the reference solution.     

A general Isserlis theorem for mixed-Gaussian random variables

This work generalizes a widely used result derived by L. Isserlis for the expectations of products of jointly Gaussian random variables by extending it to include mixed-Gaussian random variables.     

Synthesis and reactivity of unique heterocyclic structures en route to substituted diamines

Rhodium-catalyzed oxidative cyclization of allylic hydroxylamine-derived sulfamate esters furnishes a novel family of bicyclic aziridines that serve as functional precursors to substituted diamines. Investigations with the N4-Troc form of these heterocycles have led to manifold improvements in reaction performance and scope and have revealed unique differences in the stability and reactivity of such compounds dictated by the choice of N4-protecting group.     

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models

We provide an assessment of a computational strategy for protein structure refinement that combines self‐guided Langevin dynamics with umbrella‐potential biasing replica exchange using the radius of gyration as a coordinate (R_g‐ReX). Eight structurally nonredundant proteins and their decoys were examined by sampling conformational space at room temperature using the CHARMM22/GBMV2 force field to generate the ensemble of structures. Two atomic statistical potentials (RWplus and DFIRE) were analyzed for structure identification and compared to the simulation force‐field potential. The results show that, while the R_g‐ReX simulations were able to sample conformational basins that were more structurally similar to the X‐ray crystallographic structures than the starting first‐order ranked decoys, the potentials failed to detect these basins from refinement. Of the three potential functions, RWplus yielded the highest accuracy for recognition of structures that refined to an average of nearly 20% increase in native contacts relative to the starting decoys. The overall performance of R_g‐ReX is compared to an earlier study of applying temperature‐based replica exchange to refine the same decoy sets and highlights the general challenge of achieving consistently the sampling and detection threshold of 70% fraction of native contacts. © 2013 Wiley Periodicals, Inc.     

Rapid activation product separations from fission products and soil matrixes

A rapid method for the separation and qualitative analysis of several neutron activation products (¹⁹⁸Au, ¹⁹²Ir, ⁷²Ga, ⁵¹Cr, ^191/195m/197Pt, ⁵⁴Mn, ⁵⁷Co, and ⁵⁹Fe) from fission products and soil matrixes has been developed. Analytes were isolated within 20 h using ion exchange chromatography. After separation, the activation products were characterized by γ-spectroscopy and inductively coupled plasma-optical emission spectroscopy. Validation experiments demonstrated versatility of the method, showing that the activation products could be isolated from fresh fission products and other contaminants associated with complex soil matrixes.

     

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein–ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTO DOCK , and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein–ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol⁻¹ (2.177 kcal mol⁻¹) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTO DOCK , version 3.0. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1639–1662, 1998     

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand‐protein complexes and a cross‐docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid‐based docking method and a modification of the flexible sidechain technique. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009