Near-equilibrium measurements of nonequilibrium free energy

A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a nonequilibrium ensemble is that it is larger than that of the same system at equilibrium. Herein, we derive a formally exact expression for the probability distribution of a driven system, which involves path ensemble averages of the work over trajectories of the time-reversed system. From this we find a simple near-equilibrium approximation for the free energy in terms of an excess mean time-reversed work, which can be experimentally measured on real systems. With analysis and computer simulation, we demonstrate the accuracy of our approximations for several simple models.     

Mechanisms for the selective gas-phase fragmentation reactions of methionine side chain fixed charge sulfonium ion containing peptides

To enable the development of improved tandem mass spectrometry based methods for selective proteome analysis, the mechanisms, product ion structures, and other factors influencing the gas-phase fragmentation reactions of methionine side-chain derivatized "fixed-charge" phenacylsulfonium ion containing peptide ions have been examined. Dissociation of these peptide ions results in the exclusive characteristic loss of the derivatized side chain, thereby enabling their selective identification. The resultant product ion(s) are then subjected to further dissociation to obtain sequence information for subsequent protein identification. Molecular orbital calculations (at the B3LYP/6-31 + G (d,p) level of theory) performed on a simple peptide model, together with experimental evidence obtained by multistage dissociation of a regioselectively deuterated methionine derivatized sulfonium ion containing tryptic peptide, indicate that fragmentation of the fixed charge containing peptide ions occurs via SN2 reactions involving the N- and C-terminal amide bonds adjacent to the methionine side chain, resulting in the formation of stable cyclic five- and six-membered iminohydrofuran and oxazine product ions, respectively. These studies further indicate that the rings formed via these neighboring group reactions are stable to further dissociation by MS3. As a consequence, the formation of b- or y-type sequence ions are "skipped" at the site of cyclization. Despite this, complete sequence information is still obtained because of the presence of both cyclic products.     

Advanced analytical methods for the structure elucidation of polystyrene-b-poly(n-butyl acrylate) block copolymers prepared by reverse iodine transfer polymerisation

Reverse iodine transfer polymerisation (RITP) is a living radical polymerisation technique that has shown to be feasible in synthesising segmented styrene-acrylate copolymers. Polymers synthesised via RITP are typically only described regarding their bulk properties using nuclear magnetic resonance spectroscopy and size exclusion chromatography. To fully understand the complex composition of the polymerisation products and the RITP reaction mechanism, however, it is necessary to use a combination of advanced analytical methods. In the present RITP procedure, polystyrene was synthesised first and then used as a macroinitiator to synthesise polystyrene-block-poly(n-butyl acrylate) (PS-b-PBA) block copolymers. For the first time, these PS-b-PBA block copolymers were analysed by a combination of SEC, in situ¹H NMR and HPLC. ¹H NMR was used to determine the copolymer composition and the end group functionality of the samples, while SEC and HPLC were used to confirm the formation of block copolymers. Detailed information on the living character of the RITP process was obtained.     

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS³ in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically ‘trigger’ the acquisition of an MS³ spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II.     

A pyrophosphate-responsive gadolinium(III) MRI contrast agent

This study shows that the relaxivity and optical properties of functionalised lanthanide‐DTPA‐bis‐amide complexes (lanthanide=Gd³⁺ and Eu³⁺, DTPA=diethylene triamine pentaacetic acid) can be successfully modulated by addition of specific anions, without direct Ln³⁺/anion coordination. Zinc(II)‐dipicolylamine moieties, which are known to bind strongly to phosphates, were introduced in the amide “arms” of these ligands, and the interaction of the resulting Gd–Zn₂ complexes with a range of anions was screened by using indicator displacement assays (IDAs). Considerable selectivity for polyphosphorylated species (such as pyrophosphate and adenosine‐5′‐triphosphate (ATP)) over a range of other anions (including monophosphorylated anions) was apparent. In addition, we show that pyrophosphate modulates the relaxivity of the gadolinium(III) complex, this modulation being sufficiently large to be observed in imaging experiments. To establish the binding mode of the pyrophosphate and gain insight into the origin of the relaxometric modulation, a series of studies including UV/Vis and emission spectroscopy, luminescence lifetime measurements in H₂O and D₂O, ¹⁷O and ³¹P NMR spectroscopy and nuclear magnetic resonance dispersion (NMRD) studies were carried out.     

Dynamic kinetic resolution of 2-methyl-2-nitrocyclohexanol: Combining the intramolecular nitroaldol (Henry) reaction & lipase-catalysed resolution

Efforts to combine the intramolecular nitroaldol reaction with lipase-catalysed resolution of the resulting nitroaldol adduct in a one-pot dynamic kinetic resolution (DKR) are described. Significant challenges were encountered in the combination of the two systems. trans-2-Methyl-2-nitrocyclohexyl acetate (±)-3b was isolated in excellent enantiopurity (>98% ee) via a sequential DKR sequence where the lipase-mediated resolution and base-mediated interconversion of 2-methyl-2-nitrocyclohexanol 2 were effected alternately, demonstrating the feasibility of this approach initially. Further work showed, for the first time, evidence that a DKR-type system is possible for 2. Reaction engineering allowed the design of a sequential one-pot reaction system which furnished the products with excellent enantioselectivity, and good diastereoselectivity.     

A cube in a tetrahedron: microwave-assisted synthesis of an octametallic Fe(III) cluster

The microwave-assisted reaction of Fe(O2CMe)2 with salicylaldoxime (saoH2) in pyridine produces an octametallic cluster in crystalline form in 2 min. The core describes a cube encapsulated in a tetrahedron, while sao2- exhibits a novel coordination mode.     

The chemical synthesis of beta-(1-->4)-linked D-mannobiose and D-mannotriose

A D-cellobiose derivative was converted to D-mannobiose via simultaneous epimerization at C-2 and C-2'. Subsequent beta-D-glucosylation and epimerization at C-2" gave D-mannotriose.     

Synthesis and structure of [(Sn(mu-PCy))3(Na x PMDETA)2], containing an electron-deficient [(Sn(mu-PCy))3]2- dianion

The reaction of CyPHNa with Sn(NMe2)2 in the presence of PMDETA (= (Me2NCH2CH2)2NMe) gives the title compound [(Sn(mu-PCy))3(Na x PMDETA)2] (1), containing an electron-deficient [(Sn(mu-PCy))]3(2-) dianion with a novel two-electron, three centre (2e-3c) bonding arrangement.     

Contributions of quantum chemistry to the development of ring opening polymerizations and chemical recycling

Quantum chemistry has increasingly become an integral component for the development of homogeneous catalytic processes to form polymers and to break them down. This review examines how quantum chemistry has been utilized to gain insights on mechanisms and selectivities in polymerization and depolymerization reactions by homogeneous catalysts, from some of the earliest uses of theory to the most recent efforts. Key aspects of catalysis by transition-metal catalysts, organocatalytic bases and organic acids will be highlighted.