Collisional Cross-Sections with T-Wave Ion Mobility Spectrometry without Experimental Calibration

A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference?=?0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices.

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Graphical Abstract ?

     

Structural insight into the inactivation of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> non-classical transpeptidase Ldt<Subscript>Mt2</Subscript> by biapenem and tebipenem

Background

The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb).

Results

Here, we report the X-ray crystal structures of Mtb L,D-transpeptidase-2 (Ldt_Mt2) complexed with biapenem or tebipenem. Despite significant variations in carbapenem sulfur side chains, biapenem and tebipenem ultimately form an identical adduct that docks to the outer cavity of Ldt_Mt2. We propose that this common adduct is an enzyme catalyzed decomposition of the carbapenem adduct by a mechanism similar to S-conjugate elimination by β-lyases.

Conclusion

The results presented here demonstrate biapenem and tebipenem bind to the outer cavity of Ldt_Mt2, covalently inactivate the enzyme, and subsequently degrade via an S-conjugate elimination mechanism. We discuss structure based drug design based on the findings and propose that the S-conjugate elimination can be leveraged to design novel agents to deliver and locally release antimicrobial factors to act synergistically with the carbapenem carrier.

     

Professor T. C. Papanastasiou's contributions to rheology and computational fluid mechanics

Professor T. C. Papanastasiou's contributions to rheology and computational fluid mechanics are numerous and have a lasting effect. In the short span of a professional career of about 10 years, and in such diverse places as the University of Minnesota, the University of Michigan, and the Aristotle University of Thessaloniki, he developed and implemented new ideas in the fields of rheology and computational fluid mechanics. He dealt with such important topics as: i) modelling of viscoelasticity and viscoplasticity through appropriate constitutive equations; ii) numerical techniques based on the finite element method, streamline integration, inverse of the unknown, and Newton iteration for integral-differential equations; iii) numerical simulation of important polymer processes, such as fiber spinning, film blowing, film casting, extrusion and coextrusion of polymeric liquids; iv) stability analysis of multiple flows; v) three-dimensional computational techniques for generalized Newtonian flows; vi) numerical analysis of viscoplastic flows; vii) solidification problems; viii) outflow boundary conditions, etc.His many contributions include authoring two books in the area of fluid mechanics, one for undergraduate and the other for graduate use. He was a mentor and an advisor to a dozen people, his former students, who have, in their own right, successful careers, some as professors, others as research engineers in major industries. The ideas and foundations of his work are currently pursued and studied by many researchers world-wide, and in this manner it is the most appropriate tribute to him and a guarantee that his name will be remembered for years to come.Dedicated to the memory of Professor Tasos C. Papanastasiou     

Optimization of a permeation-based microfluidic direct formic acid fuel cell (DFAFC)

A design for a passive, air-breathing microfluidic fuel cell utilizing formic acid (FA) as a fuel is described and its performance characterized. The fuel cell integrates high surface area platinum (cathode) and palladium-platinum (anode) alloy electrodes within a PDMS microfluidic network that keeps them fully immersed in a liquid electrolyte. The polymer network that comprises the device also serves as a self-supporting membrane through which FA and oxygen are supplied to the alloy anode and cathode, respectively, by passive permeation from external sources. The cell is based on a planar form-factor and in its operation exploits FA concentration gradients that form across the PDMS membrane. These latter gradients allow the device to operate stably, producing a nearly constant limiting power density of ~0.2 mW/cm2, without driven laminar flow of fluids or the incorporation of an in-channel separator between the anodic and the cathodic compartments. The power output of this elementary device in air is subject to electrolyte mass transport impacts, which can be reduced for a given design rule by decreasing the internal ohmic resistance of the cell. The results suggest that operational stability can be improved by decreasing the kinetic losses imposed on the cathode side of the cell due to FA crossover and modalities for doing so, such as by increasing the efficiency of fuel capture at the anode.     

Alteration of micromilled carbonate δ18O during Kiel Device analysis

Isotopic analysis of carbonate material has been greatly facilitated by the development of autosampling devices such as the Kiel III Carbonate Device, allowing rapid automated analysis of small sample sizes. This analysis is facilitated by holding samples and acid at temperatures around 70 °C prior to reaction. In most situations this has no measurable effect on sample powders on practical timeframes, but, when analyzing exceptionally fine-grained material produced by micromilling, the δ(18)O of both aragonite and calcite is altered by -0.1 ‰/day. Laboratories that use this technique should thoroughly test and correct for this phenomenon and avoid storing pre-weighed materials within the Kiel Device or similar drying oven prior to analysis.     

Catalytic C-H bond amination from high-spin iron imido complexes

Dipyrromethene ligand scaffolds were synthesized bearing large aryl (2,4,6-Ph(3)C(6)H(2), abbreviated Ar) or alkyl ((t)Bu, adamantyl) flanking groups to afford three new disubstituted ligands ((R)L, 1,9-R(2)-5-mesityldipyrromethene, R=aryl, alkyl). While high-spin (S=2), four-coordinate iron complexes of the type ((R)L)FeCl(solv) were obtained with the alkyl-substituted ligand varieties (for R=(t)Bu, Ad and solv=THF, OEt(2)), use of the sterically encumbered aryl-substituted ligand precluded binding of solvent and cleanly afforded a high-spin (S=2), three-coordinate complex of the type ((Ar)L)FeCl. Reaction of ((Ad)L)FeCl(OEt(2)) with alkyl azides resulted in the catalytic amination of C-H bonds or olefin aziridination at room temperature. Using a 5% catalyst loading, 12 turnovers were obtained for the amination of toluene as a substrate, while greater than 85% of alkyl azide was converted to the corresponding aziridine employing styrene as a substrate. A primary kinetic isotope effect of 12.8(5) was obtained for the reaction of ((Ad)L)FeCl(OEt(2)) with adamantyl azide in an equimolar toluene/toluene-d(8) mixture, consistent with the amination proceeding through a hydrogen atom abstraction, radical rebound type mechanism. Reaction of p-(t)BuC(6)H(4)N(3) with ((Ar)L)FeCl permitted isolation of a high-spin (S=2) iron complex featuring a terminal imido ligand, ((Ar)L)FeCl(N(p-(t)BuC(6)H(4))), as determined by (1)H NMR, X-ray crystallography, and (57)Fe Mo?ssbauer spectroscopy. The measured Fe-N(imide) bond distance (1.768(2) ?) is the longest reported for Fe(imido) complexes in any geometry or spin state, and the disruption of the bond metrics within the imido aryl substituent suggests delocalization of a radical throughout the aryl ring. Zero-field (57)Fe Mo?ssbauer parameters obtained for ((Ar)L)FeCl(N(p-(t)BuC(6)H(4))) suggest a Fe(III) formulation and are nearly identical with those observed for a structurally similar, high-spin Fe(III) complex bearing the same dipyrromethene framework. Theoretical analyses of ((Ar)L)FeCl(N(p-(t)BuC(6)H(4))) suggest a formulation for this reactive species to be a high-spin Fe(III) center antiferromagnetically coupled to an imido-based radical (J = -673 cm(-1)). The terminal imido complex was effective for delivering the nitrene moiety to both C-H bond substrates (42% yield) as well as styrene (76% yield). Furthermore, a primary kinetic isotope effect of 24(3) was obtained for the reaction of ((Ar)L)FeCl(N(p-(t)BuC(6)H(4))) with an equimolar toluene/toluene-d(8) mixture, consistent with the values obtained in the catalytic reaction. This commonality suggests the isolated high-spin Fe(III) imido radical is a viable intermediate in the catalytic reaction pathway. Given the breadth of iron imido complexes spanning several oxidation states (Fe(II)-Fe(V)) and several spin states (S=0→(3)/(2)), we propose the unusual electronic structure of the described high-spin iron imido complexes contributes to the observed catalytic reactivity.     

Structural and electric field effects of ions in aqueous nanodrops

Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (～2950-3800 cm(-1)) are reported for M(H(2)O)(35-37), with M = I(-), Cl(-), HCO(3)(-), OH(-), tetrabutyl-, tetrapropyl-, and tetramethylammonium, Cs(+), Na(+), Li(+), H(+), Ba(2+), Ca(2+), Co(2+), Mg(2+), La(3+), and Tm(3+), at 133 K. A single, broad feature is observed in the bonded-OH region of the spectra that indicates that the water network in these clusters is bulk-like and likely resembles liquid water more strongly than ice. The free-OH region for all of these clusters is dominated by peaks corresponding to water molecules that accept two and donate one hydrogen bond (AAD water molecules), indicating that AAD water molecules are more abundant at the surface of these ions than AD water molecules. A-only water molecules are present in significant abundance only for the trivalent metal cations. The frequency of the AAD free-OH stretch band shifts nearly linearly with the charge state of the ion, consistent with a Stark shift attributable to the ion's electric field. From these data, a frequency range of 3704.9-3709.7 cm(-1) is extrapolated for the free-OH of AAD water molecules at the (uncharged) bulk liquid water surface, consistent with sum-frequency generation spectroscopy experiments. Differences in both the bonded- and the free-OH regions of the spectra for these ions are attributable to ion-induced patterning of the water network that extends to the surface of the clusters, which includes water molecules in the third and fourth solvation shells; that is, these ions pattern water molecules at long distance to various extents. These spectra are simulated using two different electrostatic models previously used to calculate OH-stretch spectra of bulk water and aqueous solutions and parametrized for bonded-OH frequencies. These models qualitatively reproduce a number of features in the experimental spectra, although it is evident that more sophisticated treatment of water molecule and ion polarizability and vibrational coupling is necessary for more quantitative comparisons.     

Total synthesis of (-)-N-methylwelwitindolinone C isothiocyanate

We report the first total synthesis of (-)-N-methylwelwitindolinone C isothiocyanate. Our route features a number of key transformations, including an indolyne cyclization to assemble the [4.3.1]-bicyclic scaffold, as well as a late-stage intramolecular nitrene insertion to functionalize the C11 bridgehead carbon en route to the natural product.     

High-resolution Fourier-transform infrared spectroscopy of the ν6 and Coriolis perturbation allowed ν10 modes of ketenimine

High-resolution FTIR spectra of the short lived species ketenimine have been recorded in the region 700-1300 cm(-1) and over 1500 transitions of the ν(10) and ν(6) modes have been assigned. Effective rotational and centrifugal distortion parameters for the v(10) = 1 and v(6) = 1 (excluding K(a) = 5) states were determined by co-fitting transitions, and treating strong a- and c-axis Coriolis interactions between them. Other perturbations attributed to interactions with the v(8) = 2 and v(12) = 1 + v(8) = 1 dark-states were also observed and treated. The ν(10) transitions are predicted to be inherently very weak, but are enhanced by an intensity stealing effect with the highly IR active ν(6) mode. A mechanism for this intensity stealing in ketenimine is also detailed.     

Protein Conformation and Supercharging with DMSO from Aqueous Solution

The efficacy of dimethyl sulfoxide (DMSO) as a supercharging reagent for protein ions formed by electrospray ionization from aqueous solution and the mechanism for supercharging were investigated. Addition of small amounts of DMSO to aqueous solutions containing hen egg white lysozyme or equine myoglobin results in a lowering of charge, whereas a significant increase in charge occurs at higher concentrations. Results from both near-UV circular dichroism spectroscopy and solution-phase hydrogen/deuterium exchange mass spectrometry indicate that DMSO causes a compaction of the native structure of these proteins at low concentration, but significant unfolding occurs at ~63% and ~43% DMSO for lysozyme and myoglobin, respectively. The DMSO concentrations required to denature these two proteins in bulk solution are ~3–5 times higher than the concentrations required for the onset of supercharging, consistent with a significantly increased concentration of this high boiling point supercharging reagent in the ESI droplet as preferential evaporation of water occurs. DMSO is slightly more basic than m-nitrobenzyl alcohol and sulfolane, two other supercharging reagents, based on calculated proton affinity and gas-phase basicity values both at the B3LYP and MP2 levels of theory, and all three of these supercharging reagents are significantly more basic than water. These results provide additional evidence that the origin of supercharging from aqueous solution is the result of chemical and/or thermal denaturation that occurs in the ESI droplet as the concentration of these supercharging reagents increases, and that proton transfer reactivity does not play a significant role in the charge enhancement observed.