Theory for spin-lattice relaxation of spin probes on weakly deformable DNA

The weakly bending rod (WBR) model of double-stranded DNA (dsDNA) is adapted to analyze the internal dynamics of dsDNA as observed in electron paramagnetic resonance (EPR) measurements of the spin-lattice relaxation rate, R(1e), for spin probes rigidly attached to nucleic acid-bases. The WBR theory developed in this work models dsDNA base-pairs as diffusing rigid cylindrical discs connected by bending and twisting springs whose elastic force constants are kappa and alpha, respectively. Angular correlation functions for both rotational displacement and velocity are developed in detail so as to compute values for R(1e) due to four relaxation mechanisms: the chemical shift anisotropy (CSA), the electron-nuclear dipolar (END), the spin rotation (SR), and the generalized spin diffusion (GSD) relaxation processes. Measured spin-lattice relaxation rates in dsDNA under 50 bp in length are much faster than those calculated for the same DNAs modeled as rigid rods. The simplest way to account for this difference is by allowing for internal flexibility in models of DNA. Because of this discrepancy, we derive expressions for the spectral densities due to CSA, END, and SR mechanisms directly from a weakly bending rod model for DNA. Special emphasis in this development is given to the SR mechanism because of the lack of such detail in previous treatments. The theory developed in this paper provides a framework for computing relaxation rates from the WBR model to compare with magnetic resonance relaxation data and to ascertain the twisting and bending force constants that characterize DNA.     

Volumetric and Acoustic Properties of Phenylboronic Acid in Water at Selected Temperatures

Journal of Solution Chemistry - Measurements of density and speed of sound are reported for phenylboronic acid–water solutions for molalities ranging from 0.0098 to...     

Bound fractions of methacrylate polymers adsorbed on silica using FTIR

The H‐bonding of carbonyl groups on a series of methacrylate polymers with silanols on fumed silica was studied with transmission FTIR. The set included poly(alkyl methacrylates) with alkyl groups, (n‐C_nH_2n+1) of n = 1, 2, 4, and 12 and poly(benzyl methacrylate). Shifts in the vibrational frequencies for bound carbonyl groups (of ～20 cm^?1 lower than those found in the bulk) were observed in the adsorbed polymer samples. A series of samples with different adsorbed amounts (varying from 0.5 to 2.0 mg m^?2) of each polymer was prepared to determine the effect of the side chain on the H‐bonding. The fractions of bound carbonyls, p, for each of the methacrylate polymers studied, were calculated from a model based on the ratios of the absorption coefficients of the bound to free carbonyl resonances, X (= α_b/α_f). The X values were determined from linear regressions of the ratios of the free to bound carbonyl intensities as a function of the amounts of adsorbed polymer, M_t. The bound fractions, p, were observed to decrease with increase in adsorbed amounts and with increase in the lengths of the side chains of the methacrylate polymers, except for poly(lauryl methacrylate) (PLMA). PLMA has a very low glass transition temperature (T_g) and is likely rubbery on the surface, whereas the other polymers are likely glassy at ambient temperature. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1911–1918, 2010     

1-(Fluoroalkylidene)-1,1-bisphosphonic acids are potent and selective inhibitors of the enzymatic activity of Toxoplasma gondii farnesyl pyrophosphate synthase

α-Fluorinated-1,1-bisphosphonic acids derived from fatty acids were designed, synthesized and biologically evaluated against Trypanosoma cruzi, the etiologic agent of Chagas disease, and against Toxoplasma gondii, the agent responsible for toxoplasmosis, and also towards the target parasitic enzymes farnesyl pyrophosphate synthase of T. cruzi (TcFPPS) and T. gondii (TgFPPS). Interestingly, 1-fluorononylidene-1,1-bisphosphonic acid (compound 43) proved to be an extremely potent inhibitor of the enzymatic activity of TgFPPS at the low nanomolar range, exhibiting an IC(50) of 30 nM. This compound was two-fold more potent than risedronate (IC(50) = 74 nM) that was taken as a positive control. This enzymatic activity was associated with a strong cell growth inhibition against tachyzoites of T. gondii, with an IC(50) value of 2.7 μM.     

A Dimeric Chromium(II) Pincer as an Electron Shuttle for N=N Bond Scission

Reduction of the bis-pyrazolyl pyridine complex [CrL]₂ with 4 KC₈, followed by addition of one azobenzene (overall mole ratio 1:4:1), PhNNPh, transfers reducing equivalents to three azobenzenes, to form [K₃Cr(PhNNPh)₃]. This has three κ² PhNNPh²⁻ ligands and K⁺ bound to nitrogen atoms of azobenzene. When the stoichiometry is modified to 1:4:3, the product is changed to [K₂CrL(PhNNPh)₂], which has C₂ symmetry except for the intimate ion pairing of two K⁺ ions to reduced azobenzene nitrogen atoms, and to pyrazolate and phenyl rings. The origin of the observed delivery of reducing equivalents to several, not to a single N=N bond, is traced to the resistance of the one-electron-reduced substrate to receiving a second electron, and is thus a general phenomenon. [CrL]₂ alone is shown to be a two-electron reductant towards benzo[c]cinnoline (BCC) resulting in a product of formula [Cr₂L₂(BCC)], in which the reducing equivalents originate purely from Cr^II. An analogous study of the reaction of [CrL]₂ with azobenzene yields [Cr₂L₂(PhNNPh)(THF)], an adduct in which one THF has displaced one of four hydrazide nitrogen/Cr bonds. Together these illustrate different modes for the Cr₂L₂ unit to bind and reduce the N=N bond. Collectively, these results show that two divalent Cr, without added K⁰, have the ability to reduce the N=N bond. Further KC₈ reduction of preformed Cr₂L₂(RNNR) inevitably gives products in which K⁺ stabilizes the charge in the increasingly electron-rich nitrogen atoms, in a phenomenon which mimics proton coupled electron transfer: K⁺ performs the role of H⁺. A least-squares fit of the two singly reduced DFT structures shows that the only major change is a re-orientation of one of the two phenyl rings in order to avoid repulsion with potassium but to still allow interaction of that phenyl π system with K⁺. This shows both the impact of K⁺, being modest to nitrogen/chromium interactions, but nevertheless accommodating some π donation of phenyl to potassium. Finally, delivering increasing equivalents of KC₈ leads to complete cleavage of the N=N bond, and both N bind to three Cr^II. The varied impacts of the K⁺ electrophile on NN multiple bond reduction is discussed.