SPECTRa: the deposition and validation of primary chemistry research data in digital repositories

The SPECTRa (Submission, Preservation and Exposure of Chemistry Teaching and Research Data) project has investigated the practices of chemists in archiving and disseminating primary chemical data from academic research laboratories. To redress the loss of the large amount of data never archived or disseminated, we have developed software for data publication into departmental and institutional Open Access digital repositories (DSpace). Data adhering to standard formats in selected disciplines (crystallography, NMR, computational chemistry) is transformed to XML (CML, Chemical Markup Language) which provides added validation. Context-specific chemical metadata and persistent Handle identifiers are added to enable long-term data reuse. It was found essential to provide an embargo mechanism, and policies for operating this and other processes are presented.     

Spectroscopic investigation of β-cyclodextrin -metoprolol tartrate inclusion complexes

Aqueous-solution complexes of β-cyclodextrin (β-CD) with metoprolol tartrate (MET) have been analysed with ¹H NMR and UV–vis spectroscopy. With ¹H NMR a [1:1] stoichiometry could be established for the β-CD-MET complex while its stability constant was determined with UV–vis spectroscopy. Powder diffraction data of a polycrystalline sample of the β-CD-MET complex show that a novel product has been formed, likely to be a β-CD-MET [1:1] inclusion complex. Also Hyperchem MM+ molecular-dynamics results suggest an inclusion complex and from ¹H NMR data it is inferred that probably the MET is docked in the CD with the formers methoxyethyl-benzene moiety in front. Mihaela Toma is Socrates/Erasmus student at UNED Madrid     

FAIR@Germany

The proposed international Facility for Antiproton and Ion Research (FAIR) at GSI-Darmstadt, will be a source of exotic radionuclidic beam and is expected to be operational in 2016. The facility will deliver 2 GeV/u to 45 GeV/u beam covering the entire range of the periodic table with the intensities three orders of magnitude higher than that available anywhere in the world today. This facility will serve all areas of fundamental sciences including nuclear physics, physics at extreme density conditions like neutron stars, plasma and laser physics, hadron physics and applied areas in chemistry, biology and material sciences. In this article, we discuss briefly the FAIR facility, with special emphasis on Indian participation.     

Smart templates for peak pattern matching with comprehensive two-dimensional liquid chromatography

Comprehensive two-dimensional liquid chromatography (LCxLC) generates information-rich but complex peak patterns that require automated processing for rapid chemical identification and classification. This paper describes a powerful approach and specific methods for peak pattern matching to identify and classify constituent peaks in data from LCxLC and other multidimensional chemical separations. The approach records a prototypical pattern of peaks with retention times and associated metadata, such as chemical identities and classes, in a template. Then, the template pattern is matched to the detected peaks in subsequent data and the metadata are copied from the template to identify and classify the matched peaks. Smart Templates employ rule-based constraints (e.g., multispectral matching) to increase matching accuracy. Experimental results demonstrate Smart Templates, with the combination of retention-time pattern matching and multispectral constraints, are accurate and robust with respect to changes in peak patterns associated with variable chromatographic conditions.     

From mass to structure: an aromaticity index for high‐resolution mass data of natural organic matter

Recent progress in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) has provided extensive molecular mass data for complex natural organic matter (NOM). Structural information can be deduced solely from the molecular masses for ions with extreme molecular element ratios, in particular low H/C ratios, which are abundant in thermally altered NOM (e.g. black carbon). In this communication we propose a general aromaticity index (AI) and two threshold values as unequivocal criteria for the existence of either aromatic (AI > 0.5) or condensed aromatic structures (AI ≥ 0.67) in NOM. AI can be calculated from molecular formulae which are derived from exact molecular masses of naturally occurring compounds containing C, H, O, N, S and P, and is especially useful for substances with aromatic cores and few alkylations. In order to test the validity of our model index, AI is applied to FTICRMS data of a NOM deep‐water sample from the Weddell Sea (Antarctica), a fulvic acid standard, and an artificial dataset of all theoretically possible molecular formulae. For graphical evaluation a ternary plot is suggested for four‐dimensional data representation. The proposed aromaticity index is a step towards structural identification of NOM and the molecular identification of polyaromatic hydrocarbons in the environment. Copyright © 2006 John Wiley & Sons, Ltd.     

Synthesis and characterization of biodegradable hydrophobic–hydrophilic hydrogel networks with a controlled swelling property

A biodegradable polymer network hydrogel system with both hydrophilic and hydrophobic components was synthesized and characterized. The hydrophilic and hydrophobic components were dextran and poly(D,L )lactic acid (PDLLA), respectively. These two polymers were chemically modified for incorporating unsaturated groups for subsequent UV crosslinking to generate a hydrogel with a three‐dimensional network structure. The effects of the reaction conditions on the synthesis of a dextran derivative of allyl isocyanate (dex‐AI) were studied. All newly synthesized materials were characterized by Fourier transform infrared and NMR. The swelling property of the hydrogels was studied in buffer solutions of different pHs. The results of this study showed that a wide‐range swelling property was obtained by changes in the dex‐AI/PDLLA composition ratio, the type and degree of unsaturated groups incorporated into dextran, and the UV photocrosslinking time. The solvent extraction effect on the swelling property of the hydrogels was also studied. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2392–2404, 2000     

“NMR invisible” aluminum species in dealuminated mordenite zeolite: a1H/27 AI TRAPDOR NMR study

Various kinds of aluminum species in dealuminated mordenite were investigated in detail, and the quadrupole coupling constants (QCCs) for aluminum atoms associated with these species were obtained by means of the newly introduced¹H/²⁷ AI TRAPWR method as well as²⁷Al magic angle spinning (MAS) nuclear magnetic resonance (NMR). QCC values of 11.3, 15.3, 13.3 and (14.0± 0.6) MHz were determined from the TRAPDOR profiles for Lewis acid sites, Bronsted acid sites (SiOHAl) and two kinds of non-framework aluminum species Al(OH) _n , respectively. The source of the “invisible Al” is discussed on the basis of the NMR experimental results.     

Novel atomic-level-based AI topological descriptors: application to QSPR/QSAR modeling

Novel atomic level AI topological indexes based on the adjacency matrix and distance matrix of a graph is used to code the structural environment of each atomic type in a molecule. These AI indexes, along with Xu index, are successfully extended to compounds with heteroatoms in terms of novel vertex degree v(m), which is derived from the valence connectivity delta(v) of Kier-Hall to resolve the differentiation of heteroatoms in molecular graphs. The multiple linear regression (MLR) is used to develop the structure-property/activity models based on the modified Xu and AI indices. The efficiency of these indices is verified by high quality QSPR/QSAR models obtained for several representative physical properties and biological activities of several data sets of alcohols with a wide range of non-hydrogen atoms. The results indicate that the physical properties studied are dominated by molecular size, but other atomic types or groups have small influences dependent on the studied properties. Among all atomic types, -OH groups seem to be most important due to hydrogen-bonding interactions. On the contrary, -OH groups play a dominant role in biological activities studied, although molecular size is also an important factor. These results indicate that both Xu and AI indices are useful model parameters for QSPR/QSAR analysis of complex compounds.     

人工智能在锂离子电池研发中的应用

锂离子电池已成为解决现代社会储能问题的最佳解决方案之一。然而,电池材料和器件开发都是复杂的多变量问题,传统的依赖研究人员进行实验的试错法在电池性能提升方面遇到了瓶颈。人工智能（AI）具有强大的高速、海量数据处理能力,是上述突破研究瓶颈的最具潜力的技术。其中,机器学习 (ML) 算法在评估多维数据变量和集合之间的组合关联方面的独特优势有望帮助研究人员发现不同因素之间的相互作用规律并阐明材料合成和设备制造的机制。本综述总结了锂离子电池传统研究方法遇到的各种挑战,并详细介绍了人工智能在电池材料研究、电池器件设计与制造、材料与器件表征、电池循环寿命与安全性评估等方面的应用。最重要的是,我们介绍了AI和ML在电池研究中面临的挑战,并讨论了它们应用的缺点和前景。我们相信,未来实验科学家、数学建模专家和AI专家之间更紧密的合作将极大地促进AI和ML方法用以解决传统方法难以克服的电池和材料问题。     

Library screening for synthetic agonists and antagonists of a Pseudomonas aeruginosa autoinducer

The autoinducer (AI) that initiates the quorum sensing (QS) signaling cascade in Pseudomonas aeruginosa is an acyl-homoserine lactone (acyl-HSL). We initiated a study of the requirements for binding of the AI to its protein effector LasR by synthesizing a library of analogs with the HSL moiety replaced with different amines and alcohols. We tested each compound for both agonist and antagonist activity using a QS-controlled reporter gene assay and found several new agonists and antagonists. A representative antagonist was further tested for its ability to inhibit virulence factors. This data progresses our understanding of the LasR-AI interaction toward the rational design of therapeutic inhibitors of QS.     

Excited-state double-proton transfer in the 7-azaindole dimer in the gas phase. 2. Cooperative nature of double-proton transfer revealed by H/D kinetic isotopic effects

The dispersed fluorescence (DF) spectra of the 7-azaindole dimer (7AI2) and deuterated dimers 7AI2-hd and 7AI2-dd, where hd and dd indicate the deuteration of an imino proton and two imino protons, have been measured in a supersonic free jet expansion. The undeuterated 7AI2-hh dimer exhibits only the tautomer fluorescence, but both the normal and tautomer fluorescence have been detected by exciting the origins of 7AI2-h*d, 7AI2-hd* and 7AI2-dd in the S1-S0 region, where h* and d* indicate the localization of the excitation on 7AI-h or 7AI-d moiety. The DF spectra indicate that 7AI2-h*d and 7AI2-hd* undergo excited-state proton/deuteron transfer (ESPDT), while excited-state double-deuteron transfer (ESDDT) occurs in 7AI2-dd. The H/D kinetic isotopic effects on ESDPT have been investigated by measuring the intensity ratios of the normal fluorescence to the tautomer fluorescence. The ESPDT rate is about 1/60th of the ESDPT rate, and the ESDDT rate is about 1/12th of the ESPDT rate, where ESPDT rate is an average of the rates for 7AI2-h*d and 7AI2-hd*. The observed H/D kinetic isotope effects imply that the ESDPT reaction of 7AI2 has a "cooperative" nature; i.e., the motion of the two moving protons strongly couples each other through the electron motions. The difference in the estimated ESPDT reaction rates, 9.8 x 10(9) and 6.9 x 109 s(-1) for 7AI2-h*d and 7AI2-hd*, respectively, is consistent with the concerted mechanism rather than the stepwise mechanism.     

The semantic smart laboratory: a system for supporting the chemical eScientist

One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project we have developed an innovative human-centred system which captures the process of a chemistry experiment from plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled in a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users, we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to describe the record of an experiment, and a storage system for the data from our lab book software. Just as the interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need to be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it can store, compared to the use of rigid relational databases.     

Excited‐State Double Proton Transfer in Model Base Pairs: The Stepwise Reaction on the Heterodimer of 7‐Azaindole Analogues

A four fused‐ring system 11‐propyl‐6H‐indolo[2,3‐b]quinoline ( 6 HIQ ) is strategically designed and synthesized; it possesses a central moiety of 7‐azaindole ( 7AI ) and undergoes excited‐state double proton transfer (ESDPT). Despite a barrierless type of ESDPT in the 6 HIQ dimer, femtosecond dynamics and a kinetic isotope effect provide indications for a stepwise ESDPT process in the 6 HIQ/7AI heterodimer, in which 6 HIQ (deuterated 6 HIQ ) delivers the pyrrolyl proton (deuteron) to 7AI (deuterated 7AI ) in less than 150 fs, forming an intermediate with a charge‐transfer‐like ion pair, followed by the transfer of a pyrrolyl proton (deuteron) from cation‐like 7AI (deuterated 7AI ) to the pyridinyl nitrogen of the anion‐like 6 HIQ (deuterated 6 HIQ ) in ～1.5±0.3 ps (3.5±0.3 ps). The barrier of second proton transfer is estimated to be 2.86 kcal mol^?1 for the 6 HIQ/7AI heterodimer.     

Inhibition of light-induced tautomerization of 7-azaindole by phenol: indications of proton-coupled electron/energy transfer quenching

The photophysical behavior of a 1:1 complex between phenol and 7-azaindole (7AI) has been investigated in methylcyclohexane solutions at temperatures in the range of 27 to -50 °C. A linear Benesi-Hildebrand plot associated with changes in absorbance of the complex with phenol concentration in the solutions ensures 1:1 stoichiometry of the produced complex. Our estimate for the value of the association constant (K(a)) of the complex is ~120 M?1 at 27 °C, and it is nearly twice compared to that for 1:1 complex between 7AI and ethanol measured under the same condition. The complexation results in dramatic quenching of the normal fluorescence of 7AI and the process is accelerated upon lowering of temperature. The measured spectra show no indication that phenol promotes tautomerization of 7AI in the excited state. We have argued that the hydrogen bonding between pyridinic N and phenolic O-H (N···O-H) is a vital structural factor responsible for quenching of 7AI fluorescence, and this idea has been corroborated by showing that under same condition the fluorescence of 7AI is enhanced in the presence of anisole. As a plausible mechanism of quenching, we have invoked a proton-coupled electron transfer (PCET) process between phenol and excited 7AI, which outweighs the competing tautomerization process. An analysis in terms of Remm-Weller model reveals that the PCET process involving phenol and excited 7AI could be energetically favorable (ΔG(ET)(0) < 0). An alternative mechanism, where quenching can occur via electronic energy transfer from the excited protonated 7AI to phenoxide ion, following a proton transfer along the N···O-H hydrogen bond, is also discussed.     

Driving the Transformation to Digital Catalysis

This invited Team Profile was created by a group of scientists working on concepts for research data management in catalysis in the Department of Inorganic Chemistry at the Fritz-Haber-Institut (FHI) der Max-Planck-Gesellschaft in Berlin. They recently published an article about their views on the ongoing digital transformation in catalysis research, in which the structure and current status of catalysis data are analyzed to highlight the benefits of FAIR data. Considering the fundamental aspects of catalysis as a kinetic phenomenon, they discuss how working methods should change to achieve a deeper understanding of the physical principles governing catalysis and discover new catalysts. “Achieving Digital Catalysis: Strategies for Data Acquisition, Storage and Use”, C. P. Marshall, J. Schumann, A. Trunschke, Angew. Chem. Int. Ed. Engl. 2023, 62, e202302971 .     

核磁共振技术测定联萘酚的对映体纯度

手性联萘酚((±)-BINOL)制备是国内高校常开设的一个实验,其产品的对映体纯度测试是实验的重要一环。以2-甲酰基苯硼酸和(S)-(?)-1-苯乙胺的混合物作为手性试剂与联萘酚发生Bull-James Assembly反应,以此设计了核磁共振氢谱(¹H NMR)测定联萘酚对映体纯度的实验。实验结果表明,通过反应生成的对映体混合物的核磁信号,能准确地计算出(±)-BINOL的对映体纯度。以选定的苯环氢核信号计算出的(R)-BINOL含量与理论ee值有着良好的线性关系(R²=0.9999)。此实验方法能够快速完成大量学生样品的测量,同时大大减少实验废液的产生量。学生通过此实验可对核磁共振技术有更进一步的了解。     

Better management of Western blotting results using professional photo management software

Western blotting is a proven technique essential to a significant proportion of molecular biology projects. However, as results accumulate over the years, managing data can become daunting. Recognizing that the needs of a scientist working with Western blotting results are conceptually the same as those of a professional photographer managing a summer's worth of wedding photos, we report here a new workflow for managing Western blotting results using professional photo management software. The workflow involves (i) scanning all film‐based results; (ii) importing the scans into the software; (iii) processing the scans; (iv) tagging the files with metadata, and (v) creating appropriate “smart‐albums.” Advantages of this system include space savings (both on our hard drives and on our desks), safer archival, quicker access, and easier sharing of the results. In addition, metadata‐based workflows improve cross‐experiment discovery and enable questions like “show me all blots labelled with antibody X” or “show me all experiments featuring protein Y”. As project size and breadth increase, workflows delegating results management to the computer will become more and more important so that scientists can keep focussing on science.