Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

Mechanistic aspects of proton chain transfer: A computational study for the green fluorescent protein chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging “water” that already has substantial negative charge.

Reversible addition fragmentation chain transfer (RAFT) polymerization : mechanism, process and applications

The present article gives an overview of the reversible addition fragmentation chain transfer (RAFT) process. RAFT is one of the most versatile living radical polymerization systems and yields polymers of predictable chain length and narrow molecular weight distribution. RAFT relies on the rapid exchange of thiocarbonyl thio groups between growing polymeric chains. The key strengths of the RAFT process for polymer design are its high tolerance of monomer functionality and reaction conditions, the wide range of well-controlled polymeric architectures achievable, and its (in-principle) non-rate-retarding nature. This article introduces the mechanism of polymerization, the range of polymer molecular weights achievable, the range of monomers in which polymerization is controlled by RAFT, the various polymeric architectures that can be obtained, the type of end-group functionalities available to RAFT-made polymers, and the process of RAFT polymerization.

Synthesis of epoxy-terminated polymers by radical polymerization using alpha-(t-butylperoxymethyl)styrene as chain transfer agent

Epoxy-terminated polystyrene has been synthesized by radical polymerization using alpha-(t-butylperoxymethyl) styrene (TPMS) as the chain transfer agent. The chain transfer constants were found to be 0.66 and 0.80 at 60 and 70 degrees C, respectively. The presence of epoxy end groups was confirmed by functional group modification of epoxide to aldehyde by treatment with BF3.Et(2)O. Thermal stability of TPMS was followed by differential scanning calorimetry and iodimetry. Thermal decomposition of TPMS in toluene follows first order kinetics with an activation energy of 23 kcal/mol. (C) 1996 John Wiley & Sons, Inc.

A strategy for synthesis of ion-bonded supramolecular star polymers by reversible addition-fragmentation chain transfer (RAFT) polymerization

We have developed a novel strategy for the preparation of ion-bonded supramolecular star polymers by RAFT polymerization. An ion-bonded star supramolecule with six functional groups was prepared from a triphenylene derivative containing tertiary amino groups and trithiocarbonate carboxylic acid, and used as the RAFT agent in polymerizations of tert-butyl acrylate (tBA) and styrene (St). Molecular weights and structures of the polymers were characterized by H-1 NMR and GPC. The results show that the polymerization possesses the character of living free-radical polymerization and the ion-bonded supramolecular star polymers PSt, PtBA, and PSt-b-PtBA, with six well-defined arms, were successfully synthesized.

Well-defined higher-molecular-weight polyacrylonitrile via RAFT technique in the presence of disulfide compounds as a source of chain transfer agent

Well-defined polyacrylonitrile with a higher number-average molecular weight (R.) up to 200,000 and a lower polydispersity index (PDI, 1.7-2.0) was firstly obtained via reversible addition-fragmentation chain transfer (RAFT) process. This was achieved by selecting a stable, easy way to prepare disulfide compound intermediates including bis(thiobenzoyl) disulfide (BTBDS) and bis(thiophenylacetoyl) disulfide (BTPADS) to react with azobis(isobutyronitrile) to directly synthesize RAFT agents in situ.

Reversible addition-fragmentation chain transfer mediated radical polymerization of asymmetrical divinyl monomers targeting hyperbranched vinyl polymers

Reversible addition-fragmentation chain transfer (RAFT) mediated radical polymerizations of allyl methacrylate and undecenyl methacrylate, compounds containing two types of vinyl groups with different reactivities, were investigated to provide hyperbranched polymers. The RAFT agent benzyl dithiobenzoate was demonstrated to be an appropriate chain-transfer agent to inhibit crosslinking and obtain polymers with moderate-to-high conversions. The polymerization of allyl methacrylate led to a polymer without branches but with five- or six-membered rings. However, poly(undecenyl methacrylate) showed an indication of branching rather than intramolecular cycles. The hyperbranched structure of poly(undecenyl methacrylate) was confirmed by a combination of H-1, C-13, H-1-H-1 correlation spectroscopy, and distortionless enhancement by polarization transfer 135 NMR spectra. The branching topology of the polymers was controlled by the variation of the reaction temperature, chain-transfer-agent concentration, and monomer conversion. The significantly lower inherent viscosities of the resulting polymers, compared with those of linear analogues, demonstrated their compact structure,

2-cyanoprop-2-yl dithiobenzoate mediated reversible addition-fragmentation chain transfer polymerization of acrylonitrile targeting a polymer with a higher molecular weight

The reversible addition-fragmentation chain transfer (RAFT) polymerization of acrylonitrile (AN) mediated by 2-cyanoprop-2-yl dithiobenzoate was first applied to synthesize polyacrylonitrile (PAN) with a high molecular weight up to 32,800 and a polydispersity index as low as 1.29. The key to success was ascribed to the optimization of the experimental conditions to increase the fragmentation reaction efficiency of the intermediate radical. In accordance with the atom transfer radical polymerization of AN, ethylene carbonate was also a better solvent candidate for providing higher controlled/living RAFT polymerization behaviors than dimethylformamide and dimethyl sulfoxide. The various experimental parameters, including the temperature, the molar ratio of dithiobenzoate to the initiator, the molar ratio of the monomer to dithiobenzoate, the monomer concentration, and the addition of the comonomer, were varied to improve the control of the molecular weight and polydispersity index. The molecular weights of PANS were validated by gel permeation chromatography along with a universal calibration procedure and intrinsic viscosity measurements. H-1 NMR analysis confirmed the high chain-end functionality of the resultant polymers.

Dibenzyl trithiocarbonate mediated reversible addition-fragmentation chain transfer polymerization of acrylonitrile

Reversible addition-fragmentation chain transfer polymerization has been successfully applied to polymerize acrylonitrile with dibenzyl trithiocarbonate as the chain-transfer agent. The key to success is ascribed to the improvement of the interchange frequency between dormant and active species through the reduction of the activation energy for the fragmentation of the intermediate. The influence of several experimental parameters, such as the molar ratio of the chain-transfer agent to the initiator [azobis(isobutyronitrile)], the molar ratio of the monomer to the chain-transfer agent, and the monomer concentration, on the polymerization kinetics and the molecular weight as well as the polydispersity has been investigated in detail. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and H-1 NMR analyses have confirmed the chain-end functionality of the resultant polymer.

Food-chain transfer of zinc from contaminated Urtica dioica and Acer pseudoplatanus L. to Microlophium carnosum and Drepanosiphum platanoidis Schrank

This study examines the food-chain transfer of Zn from two plant species, Urtica dioica (stinging nettle) and Acer pseudoplatanus (sycamore maple), into their corresponding aphid species, Microlophium carnosum and Drepanosiphum platanoidis. The plants were grown in a hydroponic system using solutions with increasing concentrations of Zn from 0.02 to 41.9 mg Zn/l. Above-ground tissue concentrations in U. dioica and M. carnosum increased with increasing Zn exposure (p < 0.001). Zn concentrations in A. pseudoplatanus also increased with solution concentration from the control to the 9.8 mg Zn/l solution, above which concentrations remained constant. Zn concentrations in both D. platanoidis and the phloem tissue of A. pseudoplatanus were not affected by the Zn concentration in the watering solution. It appears that A. pseudoplatanus was able to limit Zn transport in the phloem, resulting in constant Zn exposure to the aphids. Zn concentrations in D. platanoidis were around three times those in M. carnosum. Concentrations of Zn in two aphid species are dependant on species and exposure.

Food-chain transfer of cadmium and zinc from contaminated Urtica dioica to Helix aspersa and Lumbricus terrestris

The present study examines the potential of Urtica dioica as an ecologically relevant species for use in ecotoxicological testing. It is prevalent in degraded ecosystems and is a food source for invertebrates. Urtica dioica grown in hydroponic solutions containing from less than 0.003 to 5.7 mg Cd/L or from 0.02 to 41.9 mg Zn/L accumulated metals resulting in leaf tissue concentrations in the range of 0.10 to 24.9 mg Cd/kg or 22.5 to 2,772.0 mg Zn/kg. No toxicological effects were apparent except at the highest concentrations tested, suggesting that this species may be an important pathway for transfer of metals to primary plant consumers. Helix aspersa and Lumbricus terrestris were fed the Cd- and Zn-rich leaves of U. dioica for six and four weeks, respectively. Cadmium and Zn body load increased with increasing metal concentration in the leaves (p < 0.001). Ratios of invertebrate metal concentration to leaf metal concentration were in the range of 1:0.03 to 1:1.4 for Cd and 1:0.2 to 1:2.8 for Zn in H. aspersa and 1:0.002 to 1:3.9 for Cd and 1:0.2 to 1:8.8 for Zn in L. terrestris. Helix aspersa Cd and Zn tissue concentrations (15.5 and 1,220.2 mg/kg, respectively) were approximately threefold those in L. terrestris when both species were fed nettle leaves with concentrations of approximately 23 mg Cd/ kg and 3,400 mg Zn/kg. Models demonstrate that L. terrestris Cd tissue concentrations (r(2) = 0.74, p < 0.001) and H. aspersa Zn tissue concentrations (r(2) = 0.69, p < 0.001) can be estimated from concentrations of Cd and Zn within the leaves of U. dioica and suggest that reasonably reproducible results can be obtained using these species for ecotoxicological testing.

Accessing chain length dependent termination rate coefficients of methyl methacrylate (MMA) via the reversible addition fragmentation chain transfer (RAFT) process

The RAFT-CLD-T methodology is demonstrated to be not only applicable to 1-substituted monomers such as styrene and acrylates, but also to 1,1-disubstituted monomers such as MMA. The chain length of the terminating macromolecules is controlled by CPDB in MMA bulk free radical polymerization at 80 degrees C. The evolution of the chain length dependent termination rate coefficient, k(t)(i,i), was constructed in a step-wise fashion, since the MMA/CPDB system displays hybrid behavior (between conventional and living free radical polymerization) resulting in initial high molecular weight polymers formed at low RAFT agent concentrations. The obtained CLD of k(t) in MMA polymerizations is compatible with the composite model for chain length dependent termination. For the initial chain-length regime, up to a degree of polymerization of 100, k(t) decreases with alpha (in the expression k(t)(i,i) = k(t)(0) . i(-alpha)) being close to 0.65 at 80 degrees C. At chain lengths exceeding 100, the decrease is less pronounced (affording an alpha of 0.15 at 80 degrees C). However, the data are best represented by a continuously decreasing nonlinear functionality implying a chain length dependent alpha.

Modeling the molecular weight distribution of block copolymer formation in a reversible addition-fragmentation chain transfer mediated living radical polymerization

Block copolymers have become an integral part of the preparation of complex architectures through self-assembly. The use of reversible addition-fragmentation chain transfer (RAFT) allows blocks ranging from functional to nonfunctional polymers to be made with predictable molecular weight distributions. This article models block formation by varying many of the kinetic parameters. The simulations provide insight into the overall polydispersities (PDIs) that will be obtained when the chain-transfer constants in the main equilibrium steps are varied from 100 to 0.5. When the first dormant block [polymer-S-C(Z)=S] has a PDI of 1 and the second propagating radical has a low reactivity to the RAFT moiety, the overall PDI will be greater than 1 and dependent on the weight fraction of each block. When the first block has a PDI of 2 and the second propagating radical has a low reactivity to the RAFT moiety, the PDI will decrease to around 1.5 because of random coupling of two broad distributions. It is also shown how we can in principle use only one RAFT agent to obtain block copolymers with any desired molecular weight distribution. We can accomplish this by maintaining the monomer concentration at a constant level in the reactor over the course of the reaction. (c) 2005 Wiley Periodicals, Inc.