Hierarchical Modeling of Entangled Polymers

Summary : We demonstrate that it is possible to link multi-chain molecular dynamics simulations with the tube model using a single chain slip-links model as a bridge. This hierarchical approach allows significant speed up of simulations, permitting us to span the time scales relevant for a comparison with the tube theory. Fitting the mean-square displacement of individual monomers in molecular dynamics simulations with the slip-spring model, we show that it is possible to predict the stress relaxation. Then, we analyze the stress relaxation from slip-spring simulations in the framework of the tube theory. In the absence of constraint release, we establish that the relaxation modulus can be decomposed as the sum of contributions from fast and longitudinal Rouse modes, and tube survival. Finally, we discuss some open questions regarding possible future directions that could be profitable in rendering the tube model quantitative, even for mildly entangled polymers.     

Versatile synthesis and mechanism of activation of S-benzoxazolyl glycosides

As a part of a program for developing new efficient procedures for stereoselective glycosylation, a range of S-benzoxazolyl (SBox) glycosides have been synthesized. The mechanistic aspects of the SBox moiety activation for glycosylation via a variety of conceptually different pathways in the presence of thiophilic, electrophilic, or metal-based promoters have been investigated.     

Rapid three-step cleavage of RNA and DNA model systems promoted by a dinuclear Cu(II) complex in methanol. energetic origins of the catalytic efficacy

A dinuclear Cu(II) complex of 1,3-bis-N(1)-(1,5,9-triazacyclododecyl)propane with an associated methoxide (2-Cu(II)(2):(-OCH(3))) was prepared, and its kinetics of reaction with an RNA model (2-hydroxypropyl-p-nitrophenyl phosphate (1, HPNPP)) and two DNA models (methyl p-nitrophenyl phosphate (3) and iso-butyl p-chlorophenyl phosphate (4)) were studied in methanol solution at (s)(s)pH 7.2 +/- 0.2. X-ray diffraction structures of 2-Cu(II)(2):(-OH)(H(2)O)(CF(3)SO(3)-)(3):0.5CH(3)CH(2)OCH(2)CH(3) and 2-Cu(II)(2):(-OH)((C(6)H(5)CH(2)O)(2)PO(2)-)(CF(3)SO(3)-)2 show the mode of coordination of the bridging -OH and H(2)O between the two Cu(II) ions in the first complex and bridging -OH and phosphate groups in the second. The kinetic studies with 1 and 3 reveal some common preliminary steps prior to the chemical one of the catalyzed formation of p-nitrophenol. With 3, and also with the far less reactive substrate (4), two relatively fast events are cleanly observed via stopped-flow kinetics. The first of these is interpreted as a binding step which is linearly dependent on [catalyst] while the second is a unimolecular step independent of [catalyst] proposed to be a rearrangement that forms a doubly Cu(II)-coordinated phosphate. The catalysis of the cleavage of 1 and 3 is very strong, the first-order rate constants for formation of p-nitrophenol from the complex being approximately 0.7 s(-1) and 2.4 x 10(-3) s(-1), respectively. With substrate 3, 2-Cu(II)(2):(-OCH(3)) exhibits Michaelis-Mentin kinetics with a k(cat)/K(M) value of 30 M(-1) s(-1) which is 3.8 x 10(7)-fold greater than the methoxide promoted reaction of 3 (7.9 x 10(-7) M(-1) s(-1)). A free energy calculation indicates that the binding of 2-Cu(II)(2):(-OCH(3)) to the transition states for 1 and 3 cleavage stabilizes them by -21 and -24 kcal/mol, respectively, relative to that of the methoxide promoted reactions. The results are compared with a literature example where the cleavage of 1 in water is promoted by a dinuclear Zn(II) catalyst, and the energetic origins of the exalted catalysis of the 2-Cu(II)(2) and 2-Zn(II)(2) methanol systems are discussed.     

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

Background  

The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation.     

Mono- and Diamination of 4,6-Dichloropyrimidine, 2,6-Dichloropyrazine and 1,3-Dichloroisoquinoline with Adamantane-Containing Amines

N-heteroaryl substituted adamantane-containing amines are of substantial interest for their perspective antiviral and psychotherapeutic activities. Chlorine atom at alpha-position of N-heterocycles has been substituted by the amino group using convenient nucleophilic substitution reactions with a series of adamantylalkylamines. The prototropic equilibrium in these compounds was studied using NMR spectroscopy. The introduction of the second amino substituent in 4-amino-6-chloropyrimidine, 2-amino-chloropyrazine, and 1-amino-3-chloroisoquinoline was achieved using Pd(0) catalysis.     

Regioselective synthesis of new imidazo[4,5-e][1,3]thiazino[2,3-c][1,2,4]triazines via reaction of imidazo[4,5-e][1,2,4]triazinethiones with ethyl phenylpropiolate

A method for the regioselective synthesis of imidazo[4,5-e][1,3]thiazino[2,3-c][1,2,4]triazine derivatives has been developed by the reaction of imidazotriazinethiones with ethyl phenylpropiolate upon treatment with potassium carbonate or sodium methoxide in methanol. The synthesis was accomplished by Michael-type addition of the imidazotriazinethiones to the triple bond of ethyl phenylpropiolate followed by subsequent intramolecular cyclization.     

Local-global principle for congruence subgroups of Chevalley groups

Suslin’s local-global principle asserts that if a matrix over a polynomial ring vanishes modulo the independent variable and is locally elementary then it is elementary. In this article we prove Suslin’s local-global principle for principal congruence subgroups of Chevalley groups. This result is a common generalization of the result of Abe for the absolute case and Apte, Chattopadhyay and Rao for classical groups. For the absolute case the localglobal principle was recently obtained by Petrov and Stavrova in the more general settings of isotropic reductive groups.     

Application of Full Quivers of Representations of Algebras,to Polynomial Identities

In [7 Belov , A. , Rowen , L. H. , Vishne , U. Full quivers of representations of algebras. To appear in Trans. Amer. Math. Soc.  [Google Scholar]] we introduced the notion of full quivers of representations of algebras, which are more explicit than quivers of algebras, and better suited for algebras over finite fields. Here, we consider full quivers as a combinatorial tool in order to describe PI-varieties of algebras. We apply the theory to clarify the proofs of diverse topics in the literature: Determining which relatively free algebras are weakly Noetherian, determining when relatively free algebras are finitely presented, presenting a quick proof for the rationality of the Hilbert series of a relatively free PI-algebra, and explaining counterexamples to Specht's conjecture for varieties of Lie algebras.