Numerical methods for comparing fresh and weathered oils by their FTIR spectra

Four comparison statistics ('similarity indices') for the identification of the source of a petroleum oil spill based on the ASTM standard test method D3414 were investigated. Namely, (1) first difference correlation coefficient squared and (2) correlation coefficient squared, (3) first difference Euclidean cosine squared and (4) Euclidean cosine squared. For numerical comparison, an FTIR spectrum is divided into three regions, described as: fingerprint (900-700 cm(-1)), generic (1350-900 cm(-1)) and supplementary (1770-1685 cm(-1)), which are the same as the three major regions recommended by the ASTM standard. For fresh oil samples, each similarity index was able to distinguish between replicate independent spectra of the same sample and between different samples. In general, the two first difference-based indices worked better than their parent indices. To provide samples to reveal relationships between weathered and fresh oils, a simple artificial weathering procedure was carried out. Euclidean cosine and correlation coefficients both worked well to maintain identification of a match in the fingerprint region and the two first difference indices were better in the generic region. Receiver operating characteristic curves (true positive rate versus false positive rate) for decisions on matching using the fingerprint region showed two samples could be matched when the difference in weathering time was up to 7 days. Beyond this time the true positive rate falls and samples cannot be reliably matched. However, artificial weathering of a fresh source sample can aid the matching of a weathered sample to its real source from a pool of very similar candidates.     

Effect of lysozyme adsorption on the interfacial rheology of DPPC and cholesteryl myristate films

A model tear film lipid layer composed of a binary mixture of cholesteryl myristate (CM) and 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC) was characterized using surface tension measurements, Brewster angle microscopy (BAM) and interfacial stress rheology (ISR). Isotherms showed that films containing >or=90 mol % CM have a 17-fold greater % area loss between the first and second compressions than the films with less CM. BAM images clearly showed that CM films did not expand after compression, and solid-like regions extending 1-2 mm were observed at low pressures (1 mN/m). Lipid films with or=50 mol % CM became elastic at higher surface pressures. Increasing CM content reduced the surface pressure at which the mixed film became elastic. Lysozyme adsorption into a CM film increased the compressibility and resulted in a more expanded film. Lysozyme increased the ductility of the CM/DPPC films with no film breakdown occurring up to the highest pressure measured (40 mN/m). In summary, CM increased the elasticity of the lipid films, but also caused them to become brittle and incapable of expansion following compression. Lysozyme adsorption increased the ductility and decreased the isotherm hysteresis for CM/DPPC films.     

Structure and rheology of wormlike micelles

In a semi-dilute aqueous solution under certain conditions, surfactant molecules will self assemble to form wormlike micelles. The micelles are dynamic in structure since they can break and reform, providing an additional mode of relaxation. The viscoelastic properties of the wormlike micelles can be predicted using simple theological models. For many surfactant solutions the mechanical data can be related to the optical data by the stress-optical rule. From the viscoelastic data it is possible to estimate the breaking time of the micelle. The techniques of birefringence and small angle light scattering are used to study the microstructure of a surfactant solution under simple shear and extensional flow. The sample under investigation is a solution of cetyltrimethylammonium bromide and sodium salicylate in water, with a salt to surfactant ratio of 7.7. Below a critical shear rate, the birefringence increases linearly with shear rate and the stress-optical rule is valid. The SALS patterns reveal distinctive butterfly patterns indicating that scattering is a result of concentration fluctuations that moderately couple to the flow. However, above a critical shear rate the birefringence plateaus and the stress-optical rule is no longer valid. SALS patterns show both a bright streak and a butterfly pattern. The bright streak is caused by elongated structures aligned in the direction of the flow. The oriented structures occur when the characteristic time of flow is faster than the breaking time of the micelles.Dedicated to Prof. Dr. J. Meissner on the occasion of his retirement from the chair of Polymer Physics at the Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland     

Tuning through-space interactions via the secondary coordination sphere of an artificial metalloenzyme leads to enhanced Rh(iii)-catalysis

We report computationally-guided protein engineering of monomeric streptavidin Rh(iii) artificial metalloenzyme to enhance catalysis of the enantioselective coupling of acrylamide hydroxamate esters and styrenes. Increased TON correlates with calculated distances between the Rh(iii) metal and surrounding residues, underscoring an artificial metalloenzyme''s propensity for additional control in metal-catalyzed transformations by through-space interactions.

We report computationally-guided protein engineering of monomeric streptavidin Rh(iii) artificial metalloenzyme to enhance catalysis of the enantioselective coupling of acrylamide hydroxamate esters and styrenes.

Artificial metalloenzymes (ArMs) can be made by anchoring a non-natural (metal) cofactor into a protein scaffold, with the goal of imbuing new-to-nature reactivity.¹ One of the most common ArM platforms is the biotin-tetrameric(strept)avidin (biotin-tSav) system pioneered by Whitesides and Ward.^2,3 These ArMs utilize high-affinity (up to K_D ∼10⁻¹⁴ M) interactions between tSav and biotin–metal conjugates. tSav-based ArMs have appeared in an increasing number of transition-metal catalyzed transformations.^4–6 In collaboration with the Ward group, we have previously described a tetrameric streptavidin (tSav) system containing a biotinylated Rh(iii) cofactor for the asymmetric synthesis of dihydroisoquinolones using benzhydroxamate esters and acrylate partners.⁷ Monomeric streptavidin (mSav), a streptavidin/rhizavidin hybrid designed to resist tetramerization, retains its high affinity for biotin (K_D ∼10⁻⁹ M).^8,9 We recently described the use of mSav as a new ArM,¹⁰ whose simpler topology encourages protein engineering via a site-directed mutagenesis approach.Traditional manipulation of a metal''s reactivity has been accomplished by modification of the electronic and steric properties of the bound ligands (Fig. 1a).^11,12 For example, we have documented and parsed the impact of Cp electronics and sterics on a number of Rh(iii) catalyzed transformations, by structural changes to the ligand in the primary coordination sphere of Rh.¹³ On the other hand, ArMs have traditionally been used as modifiers of a metal''s steric environment largely focusing on inducing asymmetry in the bond-forming events. Less broadly appreciated is the fact that any mutations in residues proximal to the active site may also impact the metal''s electronic properties via changes to the secondary coordination sphere (Fig. 1b), with the prospect of delivering more active catalysts for a given transformation.Open in a separate windowFig. 1Methods to modify the (a) primary and (b) secondary coordination sphere of a Rh(iii) catalyst.Previously, we described a mSav·Rh(iii) catalyst and demonstrated its use in the direct enantioselective coupling of acrylamide hydroxamate esters and styrenes.¹⁰ The reaction allows rapid access to piperidines – the most common N-heterocycle found in FDA-approved pharmaceuticals.¹⁴ One of the most interesting aspects of this reaction was our observation of a 7-fold increase in turnover number (TON) by embedding the cofactor into mSav''s active site.¹⁵ It has been a long-standing goal of ArMs to not only enable new-to-nature reactivity, but also for them to achieve the stellar kinetics of a native metalloenzyme. As these systems lack the evolutionary privilege of a natural metalloenzyme, extensive mutation of the protein scaffold may be required to find the optimal environment of the metal cofactor.Predicting the effects of specific mutations can prove very challenging, as any alterations to the protein conformation and charge distribution can impact reactivity regardless of the mutation''s distance from the active site.^16–19 In order to design a better mutant, we embarked on a collaborative experimental and computational study to define the role of the protein scaffold and how single point mutations affect reactivity. We identified two key residues that play a pivotal role in mSav·Rh(iii) ArM''s secondary coordination sphere, and have used this insight to design a more active mutant.For the purposes of this study, we focused on the mSav·Rh(iii) ArM-catalyzed coupling of methacrylamide with 4-methoxystyrene as our model reaction (Fig. 2a). Using a small model of the catalyst, the lowest energy pathway of this reaction''s proposed mechanism was generated (Fig. S9^†). The calculations were performed in Turbomole^20–32 with the M06 density functional.³³ Geometries were optimized with the def2-SVP basis set, and final electronic energies were calculated with the def2-TZVP basis set.³⁴ The conductor-like screening model (COSMO)³⁵ was used as implicit solvent with a dielectric of 80 to simulate water. These calculations predicted similar barriers for the N–H activation, the C–H activation, and the migratory insertion (differences less than 3 kcal mol⁻¹). Isotope-exchange experiments revealed that the C–H activation step is reversible, implicating the migratory insertion step as turnover-limiting.¹⁰Open in a separate windowFig. 2(a) Model transformation. (b) Snapshot of the transition state for alkene insertion illustrating key nearby residues Y112 (red), E124 (blue), and S119 (purple). (c) Computed barrier to alkene insertion in the presence and absence of phenol and acetate (shown in blue).The Cp* moiety of the Cp*^biotinRhX₂ cofactor is non-covalently localized in the active site likely due to a π–π stacking interaction with Y112 (Fig. 2b). This assignment is supported by the observation that mutant Y112A leads to lower yield and enantioselectivity.¹⁰ We hypothesized that we could further manipulate both the sterics and electronics of the Cp* moiety by either directly mutating Y112 or indirectly by mutating other residues that affect the Y112-Cp* interaction.To generate a model of mSav''s protein scaffold and active-site we used QM/DMD³⁶ – a hybrid quantum mechanics/molecular mechanics method that simulates proteins piecewise. Discrete molecular dynamics (DMD) equilibrates the entire system except for the metal and part of the substrate.³⁶ After a trajectory of ∼0.5 ns, quantum mechanics (QM) is used to optimize the metal region plus sidechains and residues immediately surrounding it. This process is repeated, providing efficient sampling of the entire protein scaffold while treating the metal environment quantum-mechanically. For this study, the migratory insertion transition state was modeled in WT by freezing the coordinates of the rhodium atom and the two carbon atoms forming a bond. For each system, five replicate simulations were run for ∼20 ns each.Residues E124 and S119 both hydrogen bond to Y112 and are in close proximity to the RhCp* catalytic site (Fig. 2b).³⁷ To estimate the electronic effects of these three residues on the reaction, an acetate ion, methanol molecule, and 4-methylphenol (p-cresol) molecule were added to a small catalyst model without constraints but initially positioned to mimic the sidechains of these residues (Fig. 2c). The migratory insertion energy barrier decreases by 2 kcal mol⁻¹ with incorporation of the three residues. However, this energy barrier decreases by an additional 3 kcal mol⁻¹ upon the deletion of the methanol molecule representing S119. Not only does this imply that these amino acid sidechains may be the primary reason for the increased activity of the protein-installed catalyst, but also suggest that a longer Y112–S119 distance is favorable, so long as no water can insert in this region and replace S119 in its H-bond with Y112. We hypothesize that the carboxylate group of E124 acts as a hydrogen bond acceptor, donating electron density to the Y112 phenol ring, which in turn donates electron density to the catalyst via π–π charge transfer. This could enhance the electron donation of the metal and decrease the energy barrier to the migratory insertion step. On the other hand, S119 acts as a hydrogen bond donor which would remove electron density from Y112 and subsequently the Rh(iii) moiety.Unfortunately, mutation of Y112 (Y112F and Y112W) results in negligible protein yields. We thus identified three flanking residues (T111, E113, H87) that may be expected to have a significant impact on Y112''s position, and one distal (T32) residue, chosen as distal mutations sometimes have significant impact (Fig. 3). Through this subset of mutants, we attempted to increase TON and establish a correlation between the Y112–Rh distance and Y112–S119 distance of the mutants and their reactivities.Open in a separate windowFig. 3Structure of mSav from two different views highlighting some of the mutated residues including their TON and enantioselectivity.We used QM/DMD to simulate a representative set of these mutants spanning a wide range of TONs measured in the experiment. The Y112–Rh and Y112–S119 distances were measured every ∼0.5 ps for every simulation. The results can be represented by a 3-dimensional plot with Y112–Rh distance on the X axis, Y112–S119 distance on the Y axis, and probability density on the Z axis (Fig. 4). We find the best correlation between TON and probability density in the conformational region where the Y112–Rh distance is the shortest and the Y112–S119 interaction is not energetically relevant.³⁸Open in a separate windowFig. 4Three-dimensional probability distributions from select mutants by simultaneous sampling of Rh–Y112 and S119–Y112 distances. Probabilities for the outlined regions are also shown.To clarify this correlation, we calculated the probability of having a Y112–S119 distance between 3.5–6 Å and a Y112–Rh distance less than 5.65 Å. This Y112–S119 distance corresponds to negligible hydrogen bonding.³⁹ Additionally, we constrained the small model catalyst shown in Fig. 5b (ref. 40) and calculated the corresponding energy barriers at different Y112–Rh distances (Fig. 5a). Since rate increases exponentially as the barrier decreases,³⁵ differences in probabilities in the region where the Y112–Rh distance is between 5.4–5.65 Å have the greatest impact on the relative TONs of our model methacrylamide styrene coupling. We conclude that mutants with increasing probability in this region provide increasing TON.Open in a separate windowFig. 5a) Theoretical dependence of migratory insertion barrier on Rh-phenol distance. (b) Small-model catalyst.Theoretically, a shorter Y112–Rh distance relative to WT would result in increased reactivity. Residue G49 is located under the Rh(iii) moiety (Fig. 6). We hypothesize that by mutating the glycine into an alanine, steric congestion would force the biotinylated Rh(iii) cofactor to shift upwards closer to the electron donating phenol side chain of residue Y112. Analyzing the critical portions of the Y112–Rh and Y112–S119 distances in tandem reveals that G49A has the highest probability density in this region (Fig. 4). Indeed, experimentally, this mutant gives 97 TON and 91% ee (Fig. 6). The combination of a short Y112–Rh distance and long Y112–S119 distance leads to an increase in reactivity. This is an approximate 3-fold improvement in the TON relative to WT. The G49A mutant serves as an experimental proof of concept that a computational analysis of an ArMs secondary coordination sphere can lead to the design of a more efficient ArM.Open in a separate windowFig. 6Snapshot of the transition state for alkene insertion highlighting the position of G49 (purple) relative to Rh. Y112 is shown in red and E124 is shown in blue.In summary, we have identified three key residues that contribute to accelerating the rate of a Rh(iii)-catalyzed reaction by electronic communication to the metal via the secondary coordination sphere. E124 hydrogen bonds to Y112 transferring electron density via π–π charge transfer, an effect that is attenuated by hydrogen bonding from S119. Optimal interaction of these residues can be described computationally by finding mutants that have multiple conformations bearing short Y112–Rh distances coupled with negligible bonding between Y112 and S119. This hypothesis was experimentally verified by a mutant that enforces a closer Y112–Rh distance leading to improved TON. This result demonstrates the use of a hypothesis-based site-directed mutagenesis of the secondary sphere residues, to optimize the metal''s electronic environment within the protein scaffold and enhance an ArM''s activity.     

Optical rheometry of multicomponent polymer liquids

Recent advances in optical rheometric techniques are described, and applications of the methods are presented that motivate their use in elucidating the structure and dynamics of complex, polymeric liquids. Spectroscopic methods, such as infrared dichroism and 2-dimensional Raman scattering, which provide information concerning bond-level orientation dynamics are presented. In addition, the combination of birefringence and stress measurements is demonstrated to be capable of extracting the component dynamics in some multicomponent systems. Examples of the use of these methods include orientation in block copolymers and compatible blends.     

Structure and dynamics of a polymer solution subject to flow-induced phase separation

Experiments combining mechanical rheometry with polarimetry (birefringence and scattering dichroism) have been conducted on a 6% solution of polystyrene (1.86x10⁶ molecular weight) in dioctyl phthalate. Birefringence is used to measure the extent of segmental orientation, whereas the dichroism is sensitive to orientation and deformation of concentration fluctuations associated with the process of flow-induced phase separation. The results indicate that these fluctuations grow predominately along the neutral (or vorticity axis) of a simple shear flow. At higher rates of shear, orientation in the flow direction is favored. The transition in orientation direction is accompanied by time-dependent behavior in the optical properties of the solution during shear and the onset of shear thickening of the viscosity and the first normal stress difference coefficient.     

Branched viscoelastic surfactant solutions and their response to elongational flow

Several years ago, Münstedt and Laun reported on the influence of branching on the elongational flow properties of polymer chains (Münstedt and Laun, 1981). They concluded that, in addition to the molecular weight distribution, the degree of branching strongly affects the degree of strain thickening of the elongational viscosity in such a way that the maximum in this material function increases with branching. In a recent paper by Lin, a ternary system of dodecyldimethylamine oxide-sodium laureth sulphate-sodium chloride surfactant solutions was investigated by CryoTEM and rheology (Lin, 1996). He reported a linear relation between the added sodium chloride and the branching of the wormlike micelles. In this paper we present an investigation of these surfactant solutions in elongational flow. Our results indicate that for branched micellar systems the presence of branching enhances the maximum of the elongational viscosity in the same manner as in the case of polymer melts.