Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.

Thionylimido Complexes

An improved route to d-block and main group NSO complexes is presented including the synthesis of the first antimony(V) complexes, (Ar₃Sb(NSO)₂), and copper examples [CuBipy(PPh₃)NSO]. The structures of eight complexes are reported. The observed variation in M–N–S bond angles is due to the combination of orbital overlap (ligand-to-metal bonding) and the degree of ionicity of the bonding.     

Synthesis and characterization of modular polyphosphonate homopolymers and copolymers

Linear polyphosphonates with the generic formula –[P(Ph)(X)OR′O]_n– (X = S or Se) have been synthesized by polycondensations of P(Ph)(NEt₂)₂ and a diol (HOR′OH = 1,4-cyclohexanedimethanol, 1,4-benzenedimethanol, tetraethylene glycol, or 1,12-dodecanediol) followed by reaction with a chalcogen. Random copolymers have been synthesized by polycondensations of P(Ph)(NEt₂)₂ and mixture of two of the diols in a 2:1:1 mol ratio followed by reaction with a chalcogen. Block copolymers with the generic formula –[P(Ph)(X)OR′O]_{(x + 2)} –[P(Ph)(X)OR′O]_{(x + 3)}– (X = S or Se) have been synthesized by the polycondensations of Et₂N[P(Ph)(X)OR′O]_{(x + 2)}P(Ph)NEt₂ oligomers with HOR′O[P(Ph)(X)OR′O]_{(x + 3)}H oligomers followed by reaction with a chalcogen. The Et₂N[P(Ph)(X)OR′O]_{(x + 2)}P(Ph)NEt₂ oligomers are prepared by the reaction of an excess of P(Ph)(NEt₂)₂ with a diol while the HOR′O[P(Ph)(X)OR′O]_{(x + 3)}H oligomers are prepared by the reaction of P(Ph)(NEt₂)₂ with an excess of the diol. In each case the excess, x is the same and determines the average block sizes. All of the polymers were characterized using ¹H, ¹³C{¹H}, and ³¹P{¹H} NMR spectroscopy, TGA, DSC, and SEC. ³¹P{¹H} NMR spectroscopy demonstrates that the random and block copolymers have the expected arrangements of monomers and, in the case of block copolymers, verifies the block sizes. All polymers are thermally stable up to ~300°C, and the arrangements of monomers in the copolymers (block vs. random) affect their degradation temperatures and T_g profiles. The polymers have weight average MWs of up to 3.8 × 10⁴ Da.     

Electronic structures of tetragonal nitrido and nitrosyl metal complexes

The standard oxidation states of central metal atoms in C _4v nitrido ([M(N)(L)₅] ^z ) complexes are four units higher than those in corresponding nitrosyls ([M(NO)(L)₅] ^z ) (L=CN: z = 3−, M = Mn, Tc, Re; z = 2−, M = Fe, Ru, Os; L = NH₃: z = 2+, M = Mn, Tc, Re; z = 3+, M = Fe, Ru, Os). Recent work has suggested that [Mn(NO)(CN)₅]³⁻ behaves electronically much closer to Mn(V)[b ₂(xy)]², the ground state of [Mn(N)(CN)₅]³⁻, than to Mn(I)[b ₂(xy)]²[e(xz,yz)]⁴. We have employed density functional theory and time-dependent density functional theory to calculate the properties of the ground states and lowest-lying excitations of [M(N)(L)₅] ^z and [M(NO)(L)₅] ^z . Our results show that [M(N)(L)₅] ^z and [M(NO)(L)₅] ^z complexes with the same z value have strikingly similar electronic structures.     

Amphipols can support the activity of a membrane enzyme

Amphipathic polymers ("amphipols") were introduced several years ago (Tribet, C.; Audebert, R.; Popot, J.-L. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 15047-15050) as an alternative method for solubilizing integral membrane proteins in stable, nativelike conformations. However, direct maintenance of full membrane protein functionality in amphipol solutions has not previously been demonstrated in the absence of added lipid or detergent. In this contribution, the first zwitterionic amphipol "PMAL-B-100" is introduced. PMAL-B-100 not only maintains membrane protein structure and solubility, but also supports the full catalytic activity of an integral membrane enzyme, diacylglycerol kinase, in the complete absence of additional lipid or detergent. All of the roles which a lipid bilayer normally plays in maintaining diacylglycerol kinase's structure and in facilitating catalysis are satisfied by the environment and interactions supplied by PMAL-B-100.     

Reversible Modulation of Surface Plasmons in Gold Nanoparticles Enabled by Surface Redox Chemistry

Switchable surface redox chemistry is demonstrated in gold@iron/iron oxide core–shell nanoparticles with ambient oxidation and plasmon‐mediated reduction to modulate the oxidation state of shell layers. The iron shell can be oxidized to iron oxide through ambient oxidation, leading to an enhancement and red‐shift of the gold surface plasmon resonance (SPR). This enhanced gold SPR can drive reduction of the iron oxide shell under broadband illumination to reversibly blue‐shift and significantly dampen gold SPR absorption. The observed phenomena provide a unique mechanism for controlling the plasmonic properties and surface chemistry of small metal nanoparticles.     

Chemical Evolution of a Bacterial Proteome

We have changed the amino acid set of the genetic code of Escherichia coli by evolving cultures capable of growing on the synthetic noncanonical amino acid L ‐β‐(thieno[3,2‐b]pyrrolyl)alanine ([3,2]Tpa) as a sole surrogate for the canonical amino acid L ‐tryptophan (Trp). A long‐term cultivation experiment in defined synthetic media resulted in the evolution of cells capable of surviving Trp→[3,2]Tpa substitutions in their proteomes in response to the 20 899 TGG codons of the E. coli W3110 genome. These evolved bacteria with new‐to‐nature amino acid composition showed robust growth in the complete absence of Trp. Our experimental results illustrate an approach for the evolution of synthetic cells with alternative biochemical building blocks.     

Synthesis of some dibenzodiazepinone derivatives as potent and m2-selective antimuscarinic compounds

Two series of 5-[[4-[4-(dialkylamino)butyl]-l-cyclohexyl]acetyl], and 5-[(dialkylamino)acyl]-10,11-dihydro-5H- dibenzo[b,e][1,4]diazepin-11-ones were synthesized as potential m2-selective ligands 1,2. Their affinity and selectivity for the muscarinic cholinergic receptor m-AChR subtypes were determined. Replacing a nitrogen with CH in the piperidine ring of 5-[[4-[4-(dialkylamino)butyl]-l-piperidinyl]acetyl]-10,11-dihydro-5H-dibenzo-[b,e][1,4]diazepin-11-ones 3 significantly altered the affinity and selectivity to the muscarinic receptor subtypes.     

Preparation,characterization, and mesophase formation of esters of ethylcellulose and methylcellulose

A range of mixed ether-esters of cellulose was prepared from partially substituted ethylcellulose and methylcellulose. The ¹³C-NMR analysis of ethylcellulose with a DS of 2.5 indicated that the hydroxyl groups at carbon six of anhydroglucose units were completely substituted. Acetylation of the ethylcellulose under different conditions yielded (acetyl) (ethyl) cellulose (AEC) samples with acetyl degree of substitution ranging from 0 to 0.5. Fully substituted (propionyl) (ethyl) cellulose (PEC) and (acetyl) (methyl) cellulose (AMC) were also prepared. Chiral nematic liquid crystals were formed in these mixed ester/ethers of cellulose in concentrated solutions of acidic solvents. The critical concentration for the phase separation of the cellulosic solutions depended on the nature of the substituent, the degree of substitution, and the solvent at a given temperature. Methylcellulose solutions in trifluoroacetic acid and dichloroacetic acid form chiral nematic liquid crystals with a left-handed helicoidal structure. The acetylated methyl cellulose samples did not show the reversal of handedness with increasing acetyl content that was previously observed for the corresponding ethylcellulose samples. © 1994 John Wiley & Sons, Inc.     

Electronic structures of Group 9 metallocorroles with axial ammines

The electronic structures of metallocorroles (tpfc)M(NH(3))(2) and (tfc)M(NH(3))(2) (tpfc is the trianion of 5,10,15-(tris)pentafluorophenylcorrole, tfc is the trianion of 5,10,15-trifluorocorrole, and M = Co, Rh, Ir) have been computed using first principles quantum mechanics [B3LYP flavor of Density Functional Theory (DFT) with Poisson-Boltzmann continuum solvation]. The geometry was optimized for both the neutral systems (formal M(III) oxidation state) and the one-electron oxidized systems (formally M(IV)). As expected, the M(III) systems have a closed shell d(6) configuration; for all three metals, the one-electron oxidation was calculated to occur from a ligand-based orbital (highest occupied molecular orbital (HOMO) of B(1) symmetry). The ground state of the formal M(IV) system has M(III)-Cπ character, indicating that the metal remains d(6), with the hole in the corrole π system. As a result the calculated M(IV/III) reduction potentials are quite similar (0.64, 0.67, and 0.56 V vs SCE for M = Ir, Rh and Co, respectively), whereas the differences would have been large for purely metal-based oxidations. Vertically excited states with substantial metal character are well separated from the ground state in one-electron-oxidized cobalt (0.27 eV) and rhodium (0.24 eV) corroles, but become closer in energy in the iridium (0.15 eV) analogues. The exact splittings depend on the chosen functional and basis set combination and vary by ~0.1 eV.