Chemical mass shifts in resonance ejection experiments in the quadrupole ion trap

Chemical mass shifts were measured in a Paul ion trap operated in the mass-selective instability scan with resonance ejection using a custom-built instrument. These shifts, which can be as much as 2%, decrease with increasing endcap electrode separation owing to changes in the higher order contributions to the electric field. They also decrease with decreasing helium buffer gas pressure. Both of these effects are analogous to those found with boundary ejection. This suggests that the previously proposed chemical mass shift mechanism based on compound-dependent collisional modification of the ejection delay produced by field faults near the endcap electrode apertures holds true also for resonance ejection. The influence of the resonance frequency on chemical mass shifts was also investigated and it is shown that at certain working points (values of the Mathieu parameter q(z) and a(z)) non-linear resonances greatly reduce the ejection delay for all ions, regardless of their chemical structures, and thus reduce the magnitude of the chemical mass shift. Energetic collisions leading to dissociation can take place at an earlier stage during the ejection process in the mass analysis scan when using resonance ejection compared with boundary ejection. This leads to even larger chemical mass shifts of fragile ions in resonance ejection. Increasing the resonance voltage amplitude can enhance this effect. The chemical mass shifts of fragile ions increase with increase in the resonance voltage amplitude, whereas negligible changes occur for structurally stable ions.     

Natural resonance structures and aromaticity of the nucleobases

Natural resonance theory (NRT) and nucleus- independent chemical shift (NICS) analyses have been applied to the standard nucleobases adenine, guanine, cytosine, uracil, and thymine. The molecular electron densities were obtained from density functional theory calculations at the B3LYP level and ab initio calculations at the HF, MP2, and CCD levels. Compared with the dominance of the two Kekulé structures in benzene, the structural modifications in the forms of endocyclic heteroatoms and exocyclic substituents introduce various degrees of charge separation in nucleobases. As a result, the leading resonance structures for cytosine, uracil, and thymine are found to be covalent structures, but their weightings decrease to ~30% in the NRT expansion. For adenine and guanine, the covalent structures have weightings of ~20%, and the leading ionic resonance structures have weightings of as high as about 8%. Methods that include electron correlation effects, B3LYP, MP2, and CCD, give smaller weightings for the covalent structures than HF. However, MP2 and CCD results often include “strange” resonance structures with connections between unbonded vicinal atoms, making DFT at the B3LYP level the better choice for calculating these molecules’ electron density. The NICS at the ring center shows that the six-membered rings in cytosine, uracil, thymine, and guanine are nonaromatic with NICS within − 3 to − 1 ppm, while it is − 7.3 ppm for the six-membered ring in adenine. The NICS of the five-membered rings of adenine and guanine is around − 12 ppm, a slight decrease from the value of − 15.0 ppm for pyrrole.     

表面等离子共振(SPR)——一种新型化学检测方法的原理

近年来,表面等离子共振(SPR)现象、由于在金属纳米材料研究以及在作为灵敏检测不同化学和生化物种信号的报告器方面有着特殊的应用价值,因而受到广泛的关注.本文较详细的介绍了表面等离子共振现象的形成机制,特别对如何利用本方法作为一种新型的物种检测报告器的有关问题做了较系统的讨论.     

An in situ temperature‐programmed XPS study of the surface chemical reactions of thiophene with Ag/titania

The Ag/titania sorbent for the ultradeep desulfurization of liquid fuels was characterized by electron spin resonance and was found to contain nearly the stoichiometric titania, without significant concentration of Ti³⁺ or the reactive oxygen species. The surface chemical reactions of thiophene adsorbed on the Ag/titania were studied by temperature‐programmed XPS from 25 to 525 °C upon in situ thermal annealing in high vacuum and in situ oxidation by oxygen gas. The titania support is not chemically reactive under those conditions. Silver oxide in the Ag/titania sorbent is converted to Ag₂ S without formation of the transient surface sulfates or sulfites and is further oxidized by molecular oxygen. Copyright © 2010 John Wiley & Sons, Ltd.     

How to properly compute the resonance energy within the ab initio valence bond theory: a response to the ZHJVL paper

Valence bond (VB) theory describes a conjugated system by a set of electron-localized Lewis resonance structures. VB assumes that the magnitude of the intramolecular electron delocalization can be measured in terms of a resonance energy (RE), taken to be the energy difference between the real conjugated system (delocalized) and the corresponding most stable virtual resonance structure (localized). Proper RE estimates within VB theory require both delocalized and localized states to be defined at the same theoretical level, and the definition of the localized state to closely correspond to the intuitive picture of the corresponding VB structure. In contrast, the VB-delocal and VB-local computational approaches adopted by Zielinski, et al. [preceding paper in this issue] used definitions for either the delocalized or the localized states which, in our view, depart from the intuitive chemical picture. Consequently, their RE estimates are much lower than seemingly appropriate experimental evaluations with which they strongly disagree. Very large basis sets approaching completeness blur the boundaries among resonance structures and result in “basis set artifact” problems within any variant of VB theory. However, block-localized wavefunction (BLW) computations with mid-size basis sets not only exhibit insignificant variations with theoretical levels, but the resulting RE estimates also are justified by comparisons with those employing experimental data and MO computations. We stress that RE differs from the aromatic stabilization energy (ASE). The RE measures the total stabilization of an aromatic system, whereas ASE measures only the part of the RE that exceeds that of appropriate conjugated (but non-aromatic) reference molecules.     

Compositional Mapping of Polymer Surfaces by Chemical Force Microscopy Down to the Nanometer Scale: Reactions in Block Copolymer Microdomains

The laterally resolved analysis of the chemical surface composition of surface-treated block copolymers by atomic force microscopy (AFM) pull-off force mapping in the force volume (FV) mode and the automated analysis of the FV data is discussed. Poly(tert-butyl acrylate) (PtBA) microdomains residing in a polystyrene (PS) matrix at the surface of cyclohexane-treated polystyrene-block-poly(tert-butyl acrylate) (PtBA-b-PS) block copolymer thin films were domain-selectively deprotected, activated and chemically modified, as also shown by fluorescence microscopy. AFM pull-off force mapping in conjunction with an automated analysis of the data provided real space evidence for the successful conversion of reactive esters located in the PtBA domains and showed that AFM and related approaches, such as chemical force microscopy (CFM), can indeed contribute to assess changes in heterogeneous surface chemical composition of polymers down to sub-50 nm length scales.     

化学反应散射共振态的实验检测与理论模拟

化学反应中的散射共振态（或称反应性共振）控制着化学反应的分支比、产物的态分布及空间分布等。反应性共振的实验检测分为间接法和直接法。从理论上,一是构造反应体系的势能面,从势能面过渡态的结构来研究散射共振态;二是计算态-态反应动力学,尤其是用寿命矩阵来研究散射共振态。本文介绍反应性散射共振态的实验检测及理论模拟方法,并对今后的发展动向作出展望。     

Understanding Trends in 27Al Chemical Shifts and Quadrupolar Coupling Constants in Chloroalkyl Aluminum [AlClx(Me)3 − x]n = 1 or 2 Compounds

The usage of alkyl aluminum compounds and related structures as co‐catalyst finds a broad range of application in homogeneous and heterogeneous catalysis. While understanding the nature of the aluminum species in solution or in solids can be a challenge, ²⁷Al solid state NMR is a powerful tool to understand the structures of Al species, but their assignment remains mostly empirical, typically by comparing chemical shifts with known compounds. In this work, the observed trends in ²⁷Al‐NMR parameters – chemical shift and quadrupolar coupling constant – of chloroalkyl aluminum compounds, a prototypical class of important Lewis activators, are traced back to their frontier orbitals and electron polarization through a natural localized molecular orbital analysis. This study thus provides guidelines to understand the nature of chemical shift and thereby assignment of possible structure.     

成像核弛豫速率和化学位移与其分子量大小和钆喷酸浓度的相关性

在测试磁共振成像(MRI)用造影剂钆喷酸葡胺(Magnevist)溶液的纵向弛豫速率和化学位移实验中, 观察到溶液中被观测核的弛豫速率加快和化学位移变化与其分子大小和造影剂浓度呈密切的相关性: 对于小分子成像核(水), 弛豫速率和化学位移都与造影剂浓度变化呈很好的线性关系; 而对于大分子成像核(PEG-2000和PEG-6000), 其化学位移和弛豫速率与造影剂浓度变化则呈非线性关系.     

A unified view of propagating and localized surface plasmon resonance biosensors

The intense colors of noble metal nanoparticles have inspired artists and fascinated scientists for hundreds of years. In this review, we describe refractive index sensing platforms based on the tunability of the localized surface plasmon resonance (LSPR) of arrays of silver nanoparticles and of single nanoparticles. Specifically, the color associated with single nanoparticles and surface-confined nanoparticle arrays will be shown to be tunable and useful as platforms for chemical and biological sensing. Finally, the LSPR nanosensor will be compared to traditional, flat surface, propagating surface plasmon resonance sensors.     

Probing Bis‐FeIV MauG: Experimental Evidence for the Long‐Range Charge‐Resonance Model

The biosynthesis of tryptophan tryptophylquinone, a protein‐derived cofactor, involves a long‐range reaction mediated by a bis‐Fe^IV intermediate of a diheme enzyme, MauG. Recently, a unique charge‐resonance (CR) phenomenon was discovered in this intermediate, and a biological, long‐distance CR model was proposed. This model suggests that the chemical nature of the bis‐Fe^IV species is not as simple as it appears; rather, it is composed of a collection of resonance structures in a dynamic equilibrium. Here, we experimentally evaluated the proposed CR model by introducing small molecules to, and measuring the temperature dependence of, bis‐Fe^IV MauG. Spectroscopic evidence was presented to demonstrate that the selected compounds increase the decay rate of the bis‐Fe^IV species by disrupting the equilibrium of the resonance structures that constitutes the proposed CR model. The results support this new CR model and bring a fresh concept to the classical CR theory.     

Mass spectrometric monitoring of change of resole structures by compounding and curing of EPDM compound

Change of resole structures in a rubber compound by compounding and curing processes were investigated using ethylene-propylene-diene terpolymer (EPDM) compound and atmospheric pressure chemical ionization-mass spectrometry (APCI-MS). Resole structures were divided into three groups of reactive, pendent, and unreactive species to examine in detail the structural changes. Reasonable resole species of the major resole species having two possible structures were determined using variations of the relative abundances by compounding and curing. Of the major resole species, there was no resole species having both terminals of methylol. It was found that resole was not simply mixed in a rubber matrix and reactive resole species were diversified and activated through the compounding process. Almost all reactive resole species participated in crosslinking reactions, but some reactive resole species still remained in the vulcanizate.     

Studies on chemical constituents of Flos Puerariae-Semen Hoveniae medicine pair by HPLC and Fourier transform ion cyclotron resonance mass spectrometry

Alcoholic liver disease is currently the most clinically concerning liver disease, which occurs from chronic alcohol abuse. Flos Puerariae and Semen Hoveniae have been used to treat alcohol drinking excessively for thousands of years in China. In this study, the ethanol extract of the medicine pair was qualitatively and quantitatively analyzed by high-performance liquid chromatography and Fourier transform ion cyclotron resonance mass spectrometry. First, the high-performance liquid chromatography fingerprint was established to obtain the overall chromatographic data of its chemical constituents. Next, high-performance liquid chromatography-mass spectrometry was applied to identify its chemical constituents. Then, the characteristic constituents were simultaneously quantified by high-performance liquid chromatography. In addition, the chemical constituents that were absorbed into rat plasma were identified by high-performance liquid chromatography-mass spectrometry. As a result, a total of 48 chemical constituents in the medicine pair were detected and identified in vitro. Meanwhile, the content of seven representative constituents, including dihydromyricetin, glycitin, genistin, tectoridin, glycitein, genistein, and tectorigenin were simultaneously determined. Furthermore, a total of 19 chemical constituents were detected in rat plasma after oral administration. In short, the chemical constituents of the medicine pair were initially investigated in this study, which will lay the foundation for the discovery of its pharmacodynamic substances in further works.     

Coherent superposition of resonance wave function in terms of weighted orthogonalized natural localized configurations

In this research, the projection technique has been applied in order to decompose the electronic wave function into its weighted orthogonalized resonance components. These components have been constructed by determinants whose orbitals are selected among natural bond orbitals. However, the procedure is general and any other localized orbitals can be used as well. Both σ and π delocalize systems have been considered in order to check the reliability of the calculated resonance weights. For π‐systems, the presented procedure could predict significant decrease of weight of certain resonance structures when the molecular planarity was destroyed. Water cyclic clusters were also tested and the results confirmed the existence of strong σ‐delocalization in the clusters. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical Studies on Formation Mechanism of Resonance States for Na＋I2→Na^＋ ＋I2^－ System

An extended linear combination of arrangement channels-scattering wave-function(LCAC-SW) quantum scattering dynamic method combined with ab initio quantum chemical calculation was used to study the forma-tion mechanism of the resonance states for the collinear Na I2→Na^ I2^- I^2- ion-pair formation process on At-en-Lanting-Los potential energy surface. The resonance energy and the resonance width or the lifetime for the first resonance peak were calculated. The resonance can be identified as the Feshbach type and the physi-cal interpretation is given. The geometric structure of the resonance state for the title system has been opti-mized.     

A new algorithm for reliable and general NMR resonance assignment

The new FLYA automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins. Backbone and side-chain assignments can be determined. All experimental data are used simultaneously, thereby exploiting optimally the redundancy present in the input peak lists and circumventing potential pitfalls of assignment strategies in which results obtained in a given step remain fixed input data for subsequent steps. Instead of prescribing a specific assignment strategy, the FLYA resonance assignment algorithm requires only experimental peak lists and the primary structure of the protein, from which the peaks expected in a given spectrum can be generated by applying a set of rules, defined in a straightforward way by specifying through-bond or through-space magnetization transfer pathways. The algorithm determines the resonance assignment by finding an optimal mapping between the set of expected peaks that are assigned by definition but have unknown positions and the set of measured peaks in the input peak lists that are initially unassigned but have a known position in the spectrum. Using peak lists obtained by purely automated peak picking from the experimental spectra of three proteins, FLYA assigned correctly 96-99% of the backbone and 90-91% of all resonances that could be assigned manually. Systematic studies quantified the impact of various factors on the assignment accuracy, namely the extent of missing real peaks and the amount of additional artifact peaks in the input peak lists, as well as the accuracy of the peak positions. Comparing the resonance assignments from FLYA with those obtained from two other existing algorithms showed that using identical experimental input data these other algorithms yielded significantly (40-142%) more erroneous assignments than FLYA. The FLYA resonance assignment algorithm thus has the reliability and flexibility to replace most manual and semi-automatic assignment procedures for NMR studies of proteins.     

Single‐ended transition state finding with the growing string method

Reaction path finding and transition state (TS) searching are important tasks in computational chemistry. Methods that seek to optimize an evenly distributed set of structures to represent a chemical reaction path are known as double‐ended string methods. Such methods can be highly reliable because the endpoints of the string are fixed, which effectively lowers the dimensionality of the reaction path search. String methods, however, require that the reactant and product structures are known beforehand, which limits their ability for systematic exploration of reactive steps. In this article, a single‐ended growing string method (GSM) is introduced which allows for reaction path searches starting from a single structure. The method works by sequentially adding nodes along coordinates that drive bonds, angles, and/or torsions to a desired reactive outcome. After the string is grown and an approximate reaction path through the TS is found, string optimization commences and the exact TS is located along with the reaction path. Fast convergence of the string is achieved through use of internal coordinates and eigenvector optimization schemes combined with Hessian estimates. Comparison to the double‐ended GSM shows that single‐ended method can be even more computationally efficient than the already rapid double‐ended method. Examples, including transition metal reactivity and a systematic, automated search for unknown reactivity, demonstrate the efficacy of the new method. This automated reaction search is able to find 165 reaction paths from 333 searches for the reaction of NH₃BH₃ and (LiH)₄, all without guidance from user intuition. © 2015 Wiley Periodicals, Inc.