Automated sample preparation method for mass spectrometry analysis on recombinant proteins

A completely automated procedure for the purification and desalting of proteins with a polyhistidine purification tag prior to mass spectrometry analysis is presented. The system is ideal for rapid quality control and optimization studies and it provides researchers with a straightforward, reliable tool for studies of recombinant proteins. Forty-eight samples can be prepared within 4.5 h and only small cultivation and buffer volumes are needed. In this proof of concept, 19,000–35,000 Da recombinant proteins from both crude and clarified cell lysates were successfully prepared for subsequent analysis by electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry as well as by gel electrophoresis.     

Cations strongly reduce electron-hopping rates in aqueous solutions

We study how the ultrafast intermolecular hopping of electrons excited from the water O1s core level into unoccupied orbitals depends on the local molecular environment in liquid water. Our probe is the resonant Auger decay of the water O1s core hole (lifetime ～3.6 fs), by which we show that the electron-hopping rate can be significantly reduced when a first-shell water molecule is replaced by an atomic ion. Decays resulting from excitations at the O1s post-edge feature (～540 eV) of 6 m LiBr and 3 m MgBr(2) aqueous solutions reveal electron-hopping times of ～1.5 and 1.9 fs, respectively; the latter represents a 4-fold increase compared to the corresponding value in neat water. The slower electron-hopping in electrolytes, which shows a strong dependence on the charge of the cations, can be explained by ion-induced reduction of water-water orbital mixing. Density functional theory electronic structure calculations of solvation geometries obtained from molecular dynamics simulations reveal that this phenomenon largely arises from electrostatic perturbations of the solvating water molecules by the solvated ions. Our results demonstrate that it is possible to deliberately manipulate the rate of charge transfer via electron-hopping in aqueous media.     

Exploration of the π-electronic structure of singlet, triplet, and quintet states of fulvenes and fulvalenes using the electron localization function

The singlet ground states and lowest triplet states of penta- and heptafulvene, their benzannulated derivatives, as well as the lowest quintet states of pentaheptafulvalenes, either the parent compound or compounds in which the two rings are intercepted by either an alkynyl or a phenyl segment, were investigated at the (U)OLYP/6-311G(d,p) density functional theory level. The influence of (anti)aromaticity was analyzed by the structure-based aromaticity index HOMA, the harmonic oscillator model of aromaticity. The extent of (anti)aromatic character was also evaluated in terms of the π-electron (de)localization as measured by the π component of the electron localization function (ELF(π)). The natural atomic orbital (NAO) occupancies were calculated in order to evaluate the degree of π-electron shift caused by the opposing electron-counting rules for aromaticity in the electronic ground state (S(0); Hückel's rule) and the first ππ* excited triplet state (T(1); Baird's rule). Pentaheptafulvalene (5) shows a shift of 0.5 π electrons from the 5-ring to the 7-ring when going from the S(0) state to the lowest quintet state (Qu(1)). The pentaheptafulvalene 5 and [5.6.7]quinarene 7 were also investigated in their 90° twisted conformations. From our study it is apparent that excitation localization in fulvalenes, but not in fulvenes, to a substantial degree is determined by aromaticity localization to triplet biradical 4n π-electron cycles. Isolated benzene rings in these compounds tend to remain as closed-shell 6π-electron cycles.     

On the origin of cis selectivity in the cyclization of N-protected 2-substituted 3-aza-5-hexenyl radicals: a density functional study

Cyclization of the N-dimethylphosphinoyl-2-methyl-3-aza-5-hexenyl radical has been studied at the UB3LYP/6-31+G(d)//UB3LYP/6-31G(d) hybrid density functional level. The corresponding radical precursor has been synthesized and found to give cis/trans ratios of up to 10/1 in reductive radical cyclizations. The relative energies of reactant and transition state conformers were determined. In discord with the Beckwith-Houk model, it has been found that chair-axial transition states, which lead to cis products, are lowest in energy, rationalizing the observed experimental diastereoselectivity.     

A Declarative Modeling Framework that Integrates Solution Methods

Constraint programming offers modeling features and solution methods that are unavailable in mathematical programming but are often flexible and efficient for scheduling and other combinatorial problems. Yet mathematical programming is well suited to declarative modeling languages and is more efficient for some important problem classes. This raises this issue as to whether the two approaches can be combined in a declarative modeling framework. This paper proposes a general declarative modeling system in which the conditional structure of the constraints shows how to integrate any “checker” and any special-purpose “solver”. In particular this integrates constraint programming and optimization methods, because the checker can consist of constraint propagation methods, and the solver can be a linear or nonlinear programming routine.     

Aromaticity Effects on the Profiles of the Lowest Triplet‐State Potential‐Energy Surfaces for Rotation about the CC Bonds of Olefins with Five‐Membered Ring Substituents: An Example of the Impact of Baird’s Rule

A density functional theory study on olefins with five‐membered monocyclic 4n and 4n+2 π‐electron substituents (C₄H₃X; X=CH⁺, SiH⁺, BH, AlH, CH₂, SiH₂, O, S, NH, and CH^?) was performed to assess the connection between the degree of substituent (anti)aromaticity and the profile of the lowest triplet‐state (T₁) potential‐energy surface (PES) for twisting about olefinic C?C bonds. It exploited both Hückel’s rule on aromaticity in the closed‐shell singlet ground state (S₀) and Baird’s rule on aromaticity in the lowest ππ* excited triplet state. The compounds CH₂?CH(C₄H₃X) were categorized as set A and set B olefins depending on which carbon atom (C2 or C3) of the C₄H₃X ring is bonded to the olefin. The degree of substituent (anti)aromaticity goes from strongly S₀‐antiaromatic/T₁‐aromatic (C₅H₄⁺) to strongly S₀‐aromatic/T₁‐ antiaromatic (C₅H₄^?). Our hypothesis is that the shapes of the T₁ PESs, as given by the energy differences between planar and perpendicularly twisted olefin structures in T₁ [ΔE(T₁)], smoothly follow the changes in substituent (anti)aromaticity. Indeed, correlations between ΔE(T₁) and the (anti)aromaticity changes of the C₄H₃X groups, as measured by the zz‐tensor component of the nucleus‐independent chemical shift ΔNICS(T₁;1)_zz, are found both for sets A and B separately (linear fits; r²=0.949 and 0.851, respectively) and for the two sets combined (linear fit; r²=0.851). For sets A and B combined, strong correlations are also found between ΔE(T₁) and the degree of S₀ (anti)aromaticity as determined by NICS(S₀,1)_zz (sigmoidal fit; r²=0.963), as well as between the T₁ energies of the planar olefins and NICS(S₀,1)_zz (linear fit; r²=0.939). Thus, careful tuning of substituent (anti)aromaticity allows for design of small olefins with T₁ PESs suitable for adiabatic Z/E photoisomerization.     

Formation and NMR spectroscopy of ω-thiol protected α,ω-alkanedithiol-coated gold nanoparticles and their usage in molecular charge transport junctions

Gold nanoparticles (AuNPs) coated with stabilizing molecular monolayers are utilized in areas ranging from life sciences to nanoelectronics. Here we present a novel and facile one-pot single phase procedure for the preparation of stable AuNPs with good dispersity, which are coated with α,ω-alkanedithiols whose outer ω-thiol is protected by a triphenylmethyl group. Using dielectrophoresis we were able to trap these AuNPs, coated with ω-thiol protecting groups, in a 20 nm gold electrode nanogap. The ω-thiol group was then deprotected under acidic conditions in situ once the AuNPs were correctly positioned in the device. The subsequent deprotection resulted in an increase of conductance by up to 3 orders of magnitude, indicating that the isolated dithiol-coated AuNPs were fused into a covalently bonded network with AuNP-molecule-AuNP as well as electrode-molecule-AuNP linkages. Furthermore, complete characterization of the AuNP surface-bonded alkanedithiols was achieved using a series of one- and two-dimensional NMR spectroscopy techniques. Our spectra of the molecule-coated AuNPs show well-resolved signals, only slightly broader than for free molecules in solution, which is in contrast to many earlier reported NMR spectral data of molecules attached to AuNPs. Complementary diffusion NMR spectroscopic experiments were performed to prove that the observed alkanedithiols are definitely surface-bonded species and do not exist in free and unattached form.