Electrophoretic dynamics of large DNA stars in polymer solutions and gels

We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.     

Kinetic and mechanistic studies of the interaction of 2-mercapto pyridine with dichloro[1-alkyl-2-(arylazo)imidazole]palladium(II) complexes

Nucleophilic substitution of Pd(RaaiR′)Cl₂ [(RaaiR′ = 1-alkyl-2-(arylazo)imidazole, p-R-C₆H₄-N=N-C₃H₂NN-1-R′; where R = H(a)/ Me(b)/ Cl(c) and R′ = Et(1)/Bz(2)] with 2-Mercaptopyridine (2-SH-Py) in acetonitrile (MeCN) at 298 K, to form [Pd₂(2-S-Py)₄], has been studied spectrophotometrically under pseudo-first-order conditions and the analyses support the nucleophilic association path. The reaction follows the rate law, Rate = {k ₀ + k [2-SH-Py] ₀ ² }[Pd(RaaiR′)Cl₂]: first order in Pd(RaaiR′)Cl₂ and second order in 2-SH-Py. The rate of the reaction follows the order: Pd(RaaiEt)Cl₂ (1) < Pd(RaaiBz)Cl₂ (2) and Pd(MeaaiR′)Cl₂ (b) < Pd(HaaiR′)Cl₂ (a) < Pd(ClaaiR′)Cl₂ (c). External addition of Cl⁻ (LiCl) and HCl suppresses the rate (Rate ∝ 1/[Cl⁻]₀ & ∝1/[HCl]₀). The reactions have been studied at different temperatures (293–308 K) and activation parameters (Δ^‡ H° and Δ ^‡ S°) of the reactions were calculated from the Eyring plot and support the proposed mechanism.     

Metal complexes of pyrimidine-derived ligands — Part 6. Bischelates of cobalt(II), nickel(II) and monochelates of copper(II) with 3, 5-dimethyl-1-(4′, 6′-dimethyl-2′-pyrimidyl)pyrazole,a potential antitumour agent

Summary Cobalt(II), nickel(II) and copper(II) complexes of 3, 5-dimethyl-1-(4, 6-dimethyl-2-pyrimidyl)pyrazole (DPymPz) have been synthesized and characterized. Magnetic and electronic spectral features show that both [M(DPymPz)₂X₂]·nH₂O [M=cobalt(II) or nickel(II), X=Cl, Br, I, SCN, NO₃, ClO₄ or BF₄ andn=0 or 2] and [Cu(DPymPz)X₂(H₂O)₂] (X=Cl, Br or SCN) are essentially octahedral species. The i.r. spectra indicate that DPymPz is a neutral bidentate ligand being the pyrazolyl and one pyrimidyl ring nitrogen. The X is bonded to the central metal ion in a majority of the complexes.Part 5: N. Saha and D. Mukherjee,Polyhedron,5, 1317 (1986).     

Characteristics of in-out intermittency in delay-coupled FitzHugh–Nagumo oscillators

We analyze a pair of delay-coupled FitzHugh–Nagumo oscillators exhibiting in-out intermittency as a part of the generating mechanism of extreme events. We study in detail the characteristics of in-out intermittency and identify the invariant subsets involved – a saddle fixed point and a saddle periodic orbit – neither of which are chaotic as in the previously reported cases of in-out intermittency. Based on the analysis of a periodic attractor possessing in-out dynamics, we can characterize the approach to the invariant synchronization manifold and the spiralling out to the saddle periodic orbit with subsequent ejection from the manifold. Due to the striking similarities, this analysis of in-out dynamics also explains in-out intermittency     

η4‐HBCC‐σ,π‐Borataallyl Complexes of Ruthenium Comprising an Agostic Interaction

Thermolysis of [Cp*Ru(PPh₂(CH₂)PPh₂)BH₂(L₂)] 1 (Cp*=η⁵‐C₅Me₅; L=C₇H₄NS₂), with terminal alkynes led to the formation of η⁴‐σ,π‐borataallyl complexes [Cp*Ru(μ‐H)B{R‐C=CH₂}(L)₂] ( 2 a – c ) and η²‐vinylborane complexes [Cp*Ru(R‐C=CH₂)BH(L)₂] ( 3 a – c ) ( 2 a , 3 a : R=Ph; 2 b , 3 b : R=COOCH₃; 2 c , 3 c : R=p‐CH₃‐C₆H₄; L=C₇H₄NS₂) through hydroboration reaction. Ruthenium and the HBCC unit of the vinylborane moiety in 2 a – c are linked by a unique η⁴‐interaction. Conversions of 1 into 3 a – c proceed through the formation of intermediates 2 a – c . Furthermore, in an attempt to expand the library of these novel complexes, chemistry of σ‐borane complex [Cp*RuCO(μ‐H)BH₂L] 4 (L=C₇H₄NS₂) was investigated with both internal and terminal alkynes. Interestingly, under photolytic conditions, 4 reacts with methyl propiolate to generate the η⁴‐σ,π‐borataallyl complexes [Cp*Ru(μ‐H)BH{R‐C=CH₂}(L)] 5 and [Cp*Ru(μ‐H)BH{HC=CH‐R}(L)] 6 (R=COOCH₃; L=C₇H₄NS₂) by Markovnikov and anti‐Markovnikov hydroboration. In an extension, photolysis of 4 in the presence of dimethyl acetylenedicarboxylate yielded η⁴‐σ,π‐borataallyl complex [Cp*Ru(μ‐H)BH{R‐C=CH‐R}(L)] 7 (R=COOCH₃; L=C₇H₄NS₂). An agostic interaction was also found to be present in 2 a – c and 5 – 7 , which is rare among the borataallyl complexes. All the new compounds have been characterized in solution by IR, ¹H, ¹¹B, ¹³C NMR spectroscopy, mass spectrometry and the structural types were unequivocally established by crystallographic analysis of 2 b , 3 a – c and 5 – 7 . DFT calculations were performed to evaluate possible bonding and electronic structures of the new compounds.     

Recursive dynamics simulator (ReDySim): A multibody dynamics solver

Recursive formulations have significantly helped in achieving real-time computations and model-based control laws. The recursive dynamics simulator (ReDySim) is a MATLAB-based recursive solver for dynamic analysis of multibody systems. ReDySim delves upon the decoupled natural orthogonal complement approach originally developed for serial-chain manipulators. In comparison to the commercially available software, dynamic analyses in ReDySim can be performed without creating solid model. The input parameters are specified in MATLAB environment. ReDySim has the capability to incorporate any control algorithm with utmost ease. In this work, the capabilities of ReDySim for solving open-loop and closed-loop systems are shown by examples of robotic gripper, KUKA KR5 industrial manipulator and four-bar mechanism. ReDySim can be downloaded for free from http://www.redysim.co.nr and can be used almost instantly.     

Dioxane Dibromide–Mediated Solvent‐Free Synthesis of Vicinal Dibromides

Structurally varied vicinal dibromides have been synthesized in high yield and good purity through highly stereoselective anti‐addition of bromine across the olefinic linkages using dioxane dibromide (DD) under solvent‐free conditions.