Limiting assumptions in molecular modeling: electrostatics

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.     

Pressure‐Induced Intersite Bi?M (M=Ru, Ir) Valence Transitions in Hexagonal Perovskites

Pressure‐induced charge transfer from Bi to Ir/Ru is observed in the hexagonal perovskites Ba_3+nBiM_2+nO_9+3n (n=0,1; M=Ir,Ru). These compounds show first‐order, circa 1 % volume contractions at room temperature above 5 GPa, which are due to the large reduction in the effective ionic radius of Bi when the 6s shell is emptied on oxidation, compared to the relatively negligible effect of reduction on the radii of Ir or Ru. They are the first such transitions involving 4d and 5d compounds, and they double the total number of cases known. Ab initio calculations suggest that magnetic interactions through very short (ca. 2.6 Å) M M bonds contribute to the finely balanced nature of their electronic states.     

Influence of supporting ligand microenvironment on the aqueous stability and visible light-induced CO-release reactivity of zinc flavonolato species

The visible light-induced CO-release reactivity of the zinc flavonolato complex [(6-Ph₂TPA)Zn(3-Hfl)]ClO₄ (1) has been investigated in 1?:?1 H₂O?:?DMSO. Additionally, the effect of ligand secondary microenvironment on the aqueous stability and visible light-induced CO-release reactivity of zinc flavonolato species has been evaluated through the preparation, characterization, and examination of the photochemistry of compounds supported by chelate ligands with differing secondary appendages, [(TPA)Zn(3-Hfl)]ClO₄ (3; TPA = tris-2-(pyridylmethyl)amine) and [(bnpapa)Zn(3-Hfl)]ClO₄ (4; bnpapa = N,N-bis((6-neopentylamino-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine)). Compound 3 undergoes reaction in 1?:?1 H₂O?:?DMSO resulting in the release of the free neutral flavonol. Irradiation of acetonitrile solutions of 3 and 4 at 419 nm under aerobic conditions results in quantitative, photoinduced CO-release. However, the reaction quantum yields under these conditions are lower than that exhibited by 1, with 4 exhibiting an especially low quantum yield. Overall, the results of this study indicate that positioning a zinc flavonolato moiety within a hydrophobic microenvironment is an important design strategy toward further developing such compounds as CO-release agents for use in biological systems.     

Transient spectroscopic characterization of the ring‐opening reaction of tetrahydrochromeno[2,3‐dimethyl]indole

Tetrahydrochromeno is a structural variant of spiropyran that undergoes a reversible ring‐opening to generate a colored nitrophenolate intermediate. Earlier work confirmed this intermediate through trimethylsilyl cyanide trapping under continuous irradiation. We have performed transient absorption spectroscopy to further characterize the mechanism of the ring‐opening reaction. Excitation at 355 nm produced a transient species with an absorption maximum at 445 nm, which we assign to the nitrophenolate unit of the ring‐opened product. The transient absorption decays after ~970 ns with small optical density changes corresponding to a 0.15 quantum yield. Exposure to oxygen did not exhibit a significant deleterious effect on the photoisomerization of the chromeno dye. Time‐dependent density functional theory corroborated spectroscopic assignments of the starting chromeno and the putative ring‐opened intermediate. The excited state behavior of this system parallels the structurally similar oxazine system reported by Raymo and coworkers. The one significant difference is the longer lifetime of the photochemically generated intermediate from chromeno. Copyright © 2015 John Wiley & Sons, Ltd.     

Photophysics of Azobenzene Constrained in a UiO Metal–Organic Framework: Effects of Pressure,Solvation and Dynamic Disorder

Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter-chromophore interactions. Furthermore, high-pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans-azobenzene chromophore, constrained in the form of the 4,4’-azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure-induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans-azobenzene remains non-fluorescent (with a quantum yield less than 10⁻⁴) despite the prevention of trans-cis isomerization by the constraining MOF structure. We propose that efficient non-radiative decay is mediated by the local, pedal-like twisting of the azo group that is evident as dynamic disorder in the crystal structure.     

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.

Excitation modes for fourier transform-ion cyclotron resonance mass spectrometry

Various geometric configurations for the excitation of coherent ion motion in Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR/MS) are analyzed (in some cases for the first time) with unified notation. The instantaneous power absorption, F v, in which v is ion velocity and F the force produced by the applied excitation electric field (harmonic, single frequency, on-resonance, in-phase), is time averaged and then set equal to the time rate of change of ion total (cyclotron + magnetron + trapping) energy, to yield a differential equation that is readily solved for the (time-dependent) amplitude of each of the various ion motions. The standard FT-ICR excitation (namely, radial dipolar) is reviewed. The effects of quadrature and radial quadrupolar excitation on ion radial (cyclotron and magnetron) motions are also reviewed. Frictional damping is shown to decrease the ion cyclotron orbital radius and trapping amplitude but increase the magnetron radius. Feedback excitation (i.e., excitation at the simultaneously detected ion cyclotron orbital frequency of the same ion packet) is introduced and analyzed as a means for exciting ions whose cyclotron frequency changes during excitation (as for relativistically shifted low-mass ions). In contrast to conventional radial dipolar excitation, axial dipolar excitation of the trapping motion leads to a mass-dependent ion motional amplitude. Parametric (i.e., axial quadrupolar) excitation is shown to produce an exponential increase in the ion motional amplitudes (hyperbolic sine and hyperbolic cosine amplitude for cyclotron and magnetron radii, respectively). More detailed consideration of parametric excitation leads to an optimal ion initial radial position in parametric-mode FT-ICRjMS.     

O−• chemical ionization of carbonyl compounds

The negative ion chemical ionization mass spectra of twentyeight C₄ to C₇ carbonyl compounds were recorded using the oxide radical anion O^?? as reagent ion. As noted earlier, the reactions occurring include H⁺ abstraction, H ₂ ^+? abstraction, H? atom displacement, and alkyl radical displacement. In addition, the [M?2H]^? ions fragment further by alkyl radical elimination. The relative importance of these reactions depends strongly on molecular structure, with the result that isomer distinction frequently is possible. Where this is not possible, as for isomeric aldehydes, the collisional charge inversion mass spectra of common product ions provides isomer distinction. The H ₂ ^+? abstraction reaction is shown to involve abstraction not only of two hydrogens from the same α-carbon but also, in part, abstraction of one hydrogen from each α-carbon.     

Research note on evaluation of the plastic deformation of beams under transverse impact

The permanent deformation of a rigid perfectly plastic beam subjected to a time-dependent line load is calculated. The beam has finite length, and the load is applied transversely in the middle of the span. At the initial time, the load is zero. Thereafter, the load has a triangular time dependence. For sufficiently large values of the peak load, static and moving plastic hinges appear, and the beam is subjected to plastic bending. Previous studies of this problem have provided a numerical solution of a system of approximate equations. In this article, a numerical solution of the system of exact equations is provided. The numerical results represent a significant improvement over those that were previously available.