Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure.     

Magnetic structure variation in manganese-oxide clusters

Negative-ion photoelectron spectroscopy and ab initio simulations are used to study the variation in magnetic structure in Mn(x)O(y) (x = 3, 4[semicolon] y = 1, 2) clusters. The ferrimagnetic and antiferromagnetic ground-state structures of Mn(x)O(y) are 0.16-1.20 eV lower in energy than their ferromagnetic isomers. The presence of oxygen thus stabilizes low-spin isomers relative to the preferred high-spin ordering of bare Mn(3) and Mn(4). Each cluster has a preferred overall magnetic moment, and no evidence is seen of competing states with different spin multiplicities. However, non-degenerate isomags, which possess the same spin multiplicity but different arrangements of local moments, do contribute additional features and peak broadening in the photoelectron spectra. Proper accounting for all possible isomags is shown to be critical for accurate computational prediction of the spectra.     

Modification of Arabinogalactan Isolated from Larix sibirica Ledeb. into Sulfated Derivatives with the Controlled Molecular Weights

The process of sulfation of arabinogalactan—a natural polysaccharide from Larix sibirica Ledeb.—with sulfamic acid in 1,4-dioxane using different activators has been studied for the first time. The dynamics of the molecular weight of sulfated arabinogalactan upon variation in the temperature and time of sulfation of arabinogalactan with sulfamic acid in 1,4-dioxane has been investigated. It has been found that, as the sulfation time increases from 10 to 90 min, the molecular weights of the reaction products grow due to the introduction of sulfate groups without significant destruction of the initial polymer and sulfation products. Sulfation at 95 °C for 20 min yields the products with a higher molecular weight than in the case of sulfation at 85 °C, which is related to an increase in the sulfation rate; however, during the further process occurring under these conditions, sulfation is accompanied by the destruction and the molecular weight of the sulfated polymer decreases. The numerical optimization of arabinogalactan sulfation process has been performed. It has been shown that the optimal parameters for obtaining a product with a high sulfur content are a sulfamic acid amount of 20 mmol per 1 g of arabinogalactan, a process temperature of 85 °C, and a process time of 2.5 h.     

Synthesis and Photophysical Properties of Alkoxysilyl Derivatives of Dibenzoylmethanatoboron Difluoride

Alkoxysilyl derivatives of dibenzoylmethanatoboron difluoride (DBMBF₂) are synthesized by the hydrosilylation reaction of the corresponding O‐allyl derivatives of DBMBF₂ with triethoxysilane. The photophysical properties of the synthesized O‐allyl and alkoxysilyl derivatives are investigated. It is found that the absorption and fluorescence spectra of the DBMBF₂ derivatives essentially depend on the position of the O‐allyl or O‐propyl alkoxysilyl substituent. The highest fluorescence quantum yield is obtained for the para‐position, whereas the substitution at the meta‐position gives the largest bathochromic shift in the fluorescence spectrum. Density functional theory calculations of the structures and time‐dependent density functional theory calculations of the gas‐phase excitation and emission energies of alkoxysilyl derivatives are performed at the PBE0/SVP level of theory. Some spectral features of para‐, ortho‐, and meta‐substituted derivatives can be adequately explained by the overlapping of two absorption bands.     

Urease adsorption and activity on magnetite nanoparticles functionalized with monofunctional and bifunctional surface layers

The surface of magnetite nanoparticles was coated with functional polysiloxane layers using reaction of hydrolytic copolycondensation of tetraethoxysilane and 3-aminopropyltriethoxysilane (or N-[3-trimethoxysilylpropyl]ethylendiamine), and also that of tetraethoxysilane, 3-aminopropyltriethoxysilane and methyltriethoxysilane (or n-propyltriethoxysilane). It was shown that these functionalized magnetically controllable particles (about 60–150 nm in size as aggregates), as opposed to magnetite, adsorb urease well from aqueous solutions (up to 1 g/g), and that the level of residual activity of adsorbed layers is up to 84 % in the case of a bifunctional sample. It was established that the activity of immobilized urease is normally gradually reduced during storage of the samples, but in the case of ethylenediamine functional group is not decreased for 45 days. The synthesized samples are promising for use as magnetically directed biocatalysts.     

Sulfonimidamides and Imidosulfuric Diamides: Compounds from an Underexplored Part of Biologically Relevant Chemical Space

Two novel solid reagents—1-sulfonimidoyl- and 1-sulfamimidoyl-3-methylimidazolium derivatives—for the synthesis of sulfonimidamides and imidosulfuric diamides, respectively, were developed. It is shown that these reagents are very effective in substitution reactions with various N- and O-nucleophiles; therefore, they significantly extend the accessibility to the chemical space covered by organosulfur(VI) compounds with S=N bonds. In addition, previously unknown imidosulfuric diamides with free imino nitrogen groups were prepared, and their physical and chemical properties were characterized (including molecular geometry, pK_a, Log P, microsomal stability, and reactivity towards typical electrophiles). Similar to other organosulfur(VI) derivatives with S=N bonds, these compounds can be considered as promising bioisosteres of amides, ureas, or sulfonamides.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

Synthesis of a new polyfluorinated vinylogue of tetrathiafulvalene through 1,3-dipolar cycloaddition of ethyl beta-bromoperfluorodithiocrotonate with dimethyl acetylenedicarboxylate

The ethyl ester of beta-bromoperfluorodithiocrotonic acid reacts with dimethyl acetylenedicarboxylate to give 1,4-difluoro-2,3-bis(trifluoromethyl)-but-2-ene-1,4-diylidene-2,2'-bis(4',5'-dicarbomethoxy-1',3'-dithiole) (4), a new type of vinylogue of tetrathiafulvalene. The thermal transformations of this compound lead, depending on the temperature, to the formation of the cyclization products: 11,14-difluoro-2,3,8,9-tetra(carbomethoxy)-12,13-bis(trifluoromethyl)-1,4,7,10-tetrathiadispiro[4.0.4.4]tetradeca-2,8,11,13-tetraene (8) or 5,8-difluoro-6,7-bis(trifluoromethyl)-2,3-bis(carboxymethyl)-1,4-benzodithiine (11).     

A Complex Pyrrolo-oxazinone and Its Iodo Derivative Isolated from a Tunicate

Two cytotoxic triphenylpyrrolo-oxazinones were isolated from a tunicate and their structures elucidated by spectral methods. Lukianol A ( = 3,7,8-tris(4-hydroxyphenyl)pyrrolo[2,1-c][1,4]oxazin-1 (1H)-one; 1 ) had MIC of 1 μg/ml in KB cytotoxicity tests; MIC value for 2 was 100 μg/ml.