Molecular mechanics and dynamics of biomolecules using a solvent continuum model

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001     

Study on Electrochemiluminesce of Ru(bpy3)2+ Immobilized in a Titania Sol‐Gel Membrane

The immobilization of tris(2,2′‐bipyridyl)ruthenium(II), Ru(bpy)₃²⁺, at a glassy carbon electrode was achieved by entrapping the Ru(bpy)₃²⁺ in a vapor deposited titania sol‐gel membrane. The electrogenerated chemiluminescence (ECL) of the immobilized Ru(bpy)₃²⁺ was studied. The Ru(bpy)₃²⁺ modified electrode showed a fast ECL response to both oxalate and proline. The ECL intensity was linearly related to concentrations of oxalate and proline over the ranges from 20 to 700 μmol L^?1 and 20 to 600 μmol L^?1, respectively. The detection limits for oxalate and proline at 3σ were 5.0 μmol L^?1 and 4.0 μmol L^?1, respectively. This electrode possessed good precision and stability for oxalate and proline determinations. The electrogenerated chemiluminescence mechanism of proline system was discussed. This work provided a new way for the immobilization of Ru(bpy)₃²⁺ and the application of titania sol‐gel membrane in electrogenerated chemiluminescence.     

1,2‐Dithioquadratato‐ und 1,2‐Dithiooxalatoindate(III)

Indium(III) chloride forms in water with potassium 1,2‐dithiooxalate (dto) and potassium 1,2‐dithiosquarate (dtsq) stable coordination compounds. Due to the higher bridging ability of the 1,2‐dithiooxalate ligand in all cases only thiooxalate bridged binuclear complexes were found. From 1,2‐dithioquadratate with an identical donor atom set mononuclear trischelates could be isolated. Five crystalline complexes, (BzlMe₃N)₄[(dto)₂In(dto)In(dto)₂] ( 1 ), (BzlPh₃P)₄[(dto)₂In(dto)In(dto)₂] ( 2 ), (BzlMe₃N)₃[In(dtsq)₃] ( 3 ), (Bu₄N)₃[In(dtsq)₃] ( 4 ) and (Ph₄P)[In(dtsq)₂(DMF)₂] ( 5 ), have been isolated and characterized by X‐ray analyses. Due to the type of the complex and the cations involved these compounds crystallize in different space groups with the following parameters: 1 , monoclinic in P2₁/c with a = 14.4035(5) Å, b = 10.8141(5) Å, c = 23.3698(9) Å, β = 124.664(2)°, and Z = 2; 2 , triclinic in P with a = 11.3872(7) Å, b = 13.6669(9) Å, c = 17.4296(10) Å, α = 88.883(5)°, β = 96.763(1)°, γ = 74.587(5)°, and Z = 1; 3 , hexagonal in R3 with a = 20.6501(16) Å, b = 20.6501(16) Å, c = 19.0706(13) Å and Z = 6; 4 , monoclinic in P2₁/c with a = 22.7650(15) Å, b = 20.4656(10) Å, c = 14.4770(9) Å, β = 101.095(5)°, and Z = 4; 5 , triclinic in P with a = 9.2227(6) Å, b = 15.3876(9) Å, c = 15.5298(9) Å, α = 110.526(1)°, β = 100.138(1)°, γ = 101.003(1)°, and Z = 2.     

Real‐time lock‐in energy loss imaging with a novel high‐speed image processing CCD video camera

We have developed a high‐speed image processing CCD video camera for real‐time energy‐loss imaging using a conventional electron microscope with an energy‐loss imaging facility. As an initial demonstration of real‐time lock‐in energy‐loss imaging, a background‐subtracted energy‐loss image was observed by attaching the high‐speed image processing CCD video camera to an analytical electron microscope equipped with a floating‐type energy‐loss imaging analyser. Copyright © 2003 John Wiley & Sons, Ltd.     

A case study in conformation design: learning by doing

Efforts are described to design simple, fully flexible but conformationally preorganised omega-hydroxy-nonanoic acids that could serve as the conformation controlling unit in analogues of the potent protein-kinase C activator aplysiatoxin. Such analogues are macrodilactones incorporating the designed omega-hydroxy-nonanoic acid and 3,4-dihydroxy-pentanoic acid, which contains the pharmacophoric groups. The design process (replacement of CH(2) groups by an oxygen atom, annelation of a six-membered ring and placement of alkyl substituents) of the omega-hydroxy-nonanoic acids was monitored by force-field calculations. In the end of this process simple analogues of aplysiatoxin are proposed in which the proper disposition of the pharmacophoric groups is secured by a conformationally flexible but preorganised template structure as part of the macrodilactone ring.     

Synthesis of a model cyclic triblock terpolymer of styrene,isoprene, and methyl methacrylate

The synthesis of a model cyclic triblock terpolymer [cyclic(S‐b‐I‐b‐MMA] of styrene (S), isoprene (I), and methyl methacrylate (MMA) was achieved by the end‐to‐end intramolecular amidation reaction of the corresponding linear α,ω‐amino acid precursor [S‐b‐I‐b‐MMA] under high‐dilution conditions. The linear precursor was synthesized by the sequential anionic polymerization of S, I, and MMA with 2,2,5,5‐tetramethyl‐1‐(3‐lithiopropyl)‐1‐aza‐2,5‐disilacyclopentane as an initiator and amine generator and 4‐bromo‐1,1,1‐trimethoxybutane as a terminator and carboxylic acid generator. The separation of the unreacted linear polymer from the cyclic terpolymer was facilitated by the transformation of the unreacted species into high molecular weight polymers by the evaporation of the reaction solvent and the continuation of the reaction under high‐concentration conditions. The intermediate materials and the final cyclic terpolymer, characterized by size exclusion chromatography, vapor pressure osmometry, thin‐layer chromatography, IR and NMR spectroscopy, exhibited high molecular weight and compositional homogeneity. Dilute‐solution viscosity measurements were used as an additional proof of the cyclic structure. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1476–1483, 2002     

Effect of synthesis method and buffer composition on the LCST of a smart copolymer of N‐isopropylacrylamide and acrylic acid

Responsive polymers have been the focus of many studies during the past decade because of their ability to change according to environmental stimuli. In this paper, we report on the development of a method to synthesize a pH/temperature‐sensitive linear copolymer, poly(N‐isopropylacrylamide‐ co‐acrylic acid)(poly(NIPAAm‐co‐AAc)), with a molecular weight of about 10⁶–10⁵ Da in water using azobisisobutyronitrile (AIBN) as the initiator. The effects of the following on the lower critical solution temperature (LCST) of the copolymer and homopolymer of NIPAAm were investigated: the type of buffer salts and pH changes of test solutions, molecular weight and concentration of homopolymer/copolymer solutions, and AAc monomer molar feed ratio (mol%). The effects of different synthesis methods on the molecular weight and on the AAc content were also evaluated. The mechanism of action in environments with different pH values is discussed. Copyright © 2007 John Wiley & Sons, Ltd.     

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Electrochemical Evaluation of the Interaction between Avidin and Biotin at Biotinylated Polypyrrole Electrode Using a Redox Marker

The interaction between avidin and biotin was evaluated electrochemically by monitoring the change in the electrode response of redox markers. Biotin was immobilized on the electrode surface by means of the electrochemical polymerization of biotinylated pyrrole and pyrrole. When avidin was introduced onto the biotinylated polypyrrole electrode surface, the large change in the electrode response of the redox marker was detected. The fact that the change in the electrode response of a marker ion could be attributed to the electrostatic interaction between avidin on the electrode surface and the redox marker ion present in a solution was verified by replacing avidin with NutrAvidin. At a pH lower than the isoelectric point of avidin, the electrode response of ferrocyanide as an anionic marker ion increased linearly within the range of 5.0×10^?9 ?3.0×10^?8 M avidin. The relative standard deviation at 1.5×10^?8 M avidin was about 5.4% (n=5). The detection of biotin was also performed using a competitive reaction between biotin in solution and biotin that had been immobilized on the electrode surface in the form of the biotinylated polypyrrole.     

Synthesis,optical, and electrochemical properties of novel copolymers on the basis of benzothiadiazole and electron‐rich arene units

Novel alternating conjugated copolymers ( P1–P6 ) consisting of an electron‐deficient benzothiadiazole and a variety of electron‐rich thiophene‐arene‐thiophene units were synthesized by palladium‐catalyzed polycondensations (Stille and Suzuki reactions), aiming at processable materials with a reduced optical band gap. The structures of P1–P6 were confirmed by ¹H NMR and ¹³C NMR, and their molecular weights were determined by size exclusion chromatography. In the Suzuki polycondensation, the role of the catalyst [Pd(PPh₃)₄ and Pd(OAc)₂] on the resulting molecular weight was investigated. Pd(OAc)₂ enhances the molecular weight of the polymers for both thiophene and phenylene bis‐boronic esters as compared with Pd(PPh₃)₄. The optical properties of the polymers were examined in solution and the solid state. The polymers with n‐octyl substituents ( P1 , P4 , P5 , and P6 ) on the thiophene rings possessed less‐planar structures as a result of torsional steric hindrance, and their absorption spectra appeared blueshifted as compared with their unsubstituted analogues ( P2 and P3 ). The electrochemical properties of the polymers were studied using cyclic voltammetry. Although the alkyl substitution affects the oxidation potential, only marginal differences in the reduction potentials were observed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2360–2372, 2002