Structures and mechanisms in chemical reactions: George A. Olah’s life-long search of chemistry

The Hungarian-born American chemistry Nobel laureate George A. Olah used superacids to give longer life to carbocations. He resolved a long-standing debate on reaction mechanism in organic chemistry and, more importantly, opened new vistas in hydrocarbon chemistry to produce hosts of new compounds. The concerted utilization of organic synthesis, physical techniques, and computational methods led to spectacular achievements in hydrocarbon chemistry. Olah has always been on the lookout for the practical applications of his discoveries in fundamental chemistry. He continued his research after his Nobel award and has worked out the idea, which he labeled “the methanol economy.” Olah’s example shows that a great researcher can also be a devoted and caring human being.     

Is there a future for computational chemistry in drug research?

Improvements in computational chemistry methods have had a growing impact on drug research. But will incremental improvements be sufficient to ensure this continues? Almost all existing efforts to discover new drugs depend on the classic one target, one drug paradigm, although the situation is changing slowly. A new paradigm that focuses on a more systems biology approach and takes account of the reality that most drugs exhibit some level of polypharmacology is beginning to emerge. This will bring about dramatic changes that can significantly influence the role that computational methods play in future drug research. But these changes require that current methods be augmented with those from bioinformatics and engineering if the field is to have a significant impact on future drug research.     

Spin frustration in 2D kagomé lattices: a problem for inorganic synthetic chemistry

A kagomé antiferromagnet presents an ideal construct for studying the unusual physics that result from the placement of magnetically frustrated spins on a low-dimensional lattice. Jarosites are the prototype for a spin-frustrated magnetic structure, because these materials are composed exclusively of kagomé layers. Notwithstanding, jarosite-type materials have escaped precise magnetic characterization over the past three decades, because they are notoriously difficult to prepare in pure and single-crystal forms. These hurdles have been overcome with the development of redox-based hydrothermal methods. Armed with pure and crystalline materials, several perplexing issues surrounding the magnetic properties of the jarosites have been resolved, yielding a detailed and comprehensive picture of the ground-state physics of this kagomé lattice.     

DNA microarrays: is there a role for analytical chemistry?

DNA microarrays, or "DNA chips", represent a relatively new technology that is having a profound impact on biology and medicine, yet analytical research into this area is somewhat sparse. This article presents an overview of DNA microarrays and their application to gene expression analysis from the perspective of analytical chemistry, treating aspects of array platforms, measurement, image analysis, experimental design, normalization, and data analysis. Typical approaches are described and unresolved issues are discussed, with a view to identifying some of the contributions that might be made by analytical chemists.     

Metrology in chemistry – a public task

 The importance of analytical chemistry is increasing in many public fields, and the demand for reliable measurement results is growing accordingly. A measurement result will be reliable only if its uncertainty has been quantified. This can be achieved only by tracing the result back to a standard realizing the unit in which the measurement result is expressed. The National Metrology Institutes (NMIs) can contribute to the reliability of the measurement results by developing measuring methods, and by providing reference materials and standard measuring devices. In fields in which the comparability of measurement results is of particular importance, they establish traceability structures. Responding to the globalization of trade and industry the International Committee for Weights and Measures (CIPM) agreed on an arrangement on the mutual recognition of calibration certificates (CIPM MRA) issued by the NMIs. Received: 19 April 2000 / Accepted: 28 July 2000     

Formal synthesis of berkelic acid: a lesson in α-alkylation chemistry

The full details of our enantioselective formal synthesis of the biologically active natural product berkelic acid are described. The insertion of the C-18 methyl group proved challenging, with three different approaches investigated to install the correct stereochemistry. Our initial Horner-Wadsworth-Emmons/oxa-Michael approach to the berkelic acid core proved unsuccessful upon translation to the natural product itself. However, addition of a silyl enol ether to an oxonium ion, followed by a one-pot debenzylation/spiroketalisation/thermodynamic equilibration procedure, afforded the tetracyclic structure of the berkelic acid core as a single diastereoisomer.     

Examining the performance of DFT methods in uranium chemistry: does core size matter for a pseudopotential?

We have investigated the performance of DFT in U(VI) chemistry. A large, representative selection of functionals has been tested, in combination with two ECPs developed in Stuttgart that have different-sized cores (60 and 78 electrons for U). In addition, several tests were undertaken with another 14 electron pseudopotential, which was developed in Los Alamos. The experimental database contained vibrational wavenumbers, thermochemical data, and (19)F chemical shifts for molecules of the type UF(6-n)Cl(n). For the prediction of vibrational wavenumbers, the large-core RECP (14 electrons) gives results that are at least as good as those obtained with the small-core RECP (32 electrons). GGA functionals are as successful as hybrid GGA for vibrational spectroscopy; typical errors are only a few percent with the Stuttgart pseudopotentials. For thermochemistry, hybrid versions of DFT are more successful than GGA, LDA, or meta-GGA. Marginally better results are obtained with a 32 electron ECP than with 14; since the experimental uncertainties are at least 25 kJ/mol for each reaction, the best functionals give results that are essentially indistinguishable from experiment. However, large-basis CCSD(T) results match experiment better than any DFT that we examined. Our findings for NMR spectroscopy are rather disappointing; no combination of pseudopotential, functional, and basis yields even a qualitatively correct prediction of trends in the (19)F chemical shifts of UF(6-n)Cl(n) species. Results yielded by the large-core RECP are, in general, slightly less bad than those obtained with the small core. We conclude that DFT cannot be recommended for predictions of NMR spectra in this series of compounds, though this conclusion should not be generalized. Our most important result concerns the good performance of the large-core Stuttgart pseudopotential. Given its computational efficiency, we recommend that it be used with DFT methods for the prediction of molecular geometries, vibrational frequencies, and thermochemistry of a given oxidation state. The hybrid GGA functionals MPW1PW91 and PBE0 give the best results overall.     

Machine learning methods for property prediction in chemoinformatics: Quo Vadis?

This paper is focused on modern approaches to machine learning, most of which are as yet used infrequently or not at all in chemoinformatics. Machine learning methods are characterized in terms of the "modes of statistical inference" and "modeling levels" nomenclature and by considering different facets of the modeling with respect to input/ouput matching, data types, models duality, and models inference. Particular attention is paid to new approaches and concepts that may provide efficient solutions of common problems in chemoinformatics: improvement of predictive performance of structure-property (activity) models, generation of structures possessing desirable properties, model applicability domain, modeling of properties with functional endpoints (e.g., phase diagrams and dose-response curves), and accounting for multiple molecular species (e.g., conformers or tautomers).     

Report of the TrainMiC® Convention, held in Celje, Slovenia (10–14 January 2009)

The main aim of the TrainMiC^® Convention was to gather TrainMiC^® authorized trainers from all 19 countries involved in this programme. About 90% of all authorized TrainMiC^® trainers assembled at this Convention, which shows the interest in and usefulness of the TrainMiC^® system. The role and position of the authorized trainers was formally recognized by the introduction of a User License Agreement (based on a European Commission Decision, concerning the granting of a copyright license for TrainMiC^® trainers, 17 December 2008) which was signed by the attendants. Participants received an update on the training material and could give their input and suggestions for improvement, which will then be discussed and reviewed by the Editorial Board. It is this which makes TrainMiC^® a truly devolved and living system which can adapt itself. Participants also gave their input on how to further develop TrainMiC^® from a system point of view. Topics included better focus on priority sectors, improved course interactivity, further improvement of pedagogical skills of authorized trainers, better marketing and identifying multiple sources of funding.     

Singlet Oxygen Sensor Green®: photochemical behavior in solution and in a mammalian cell

The development of efficient and selective luminescent probes for reactive oxygen species, particularly for singlet molecular oxygen, is currently of great importance. In this study, the photochemical behavior of Singlet Oxygen Sensor Green^® (SOSG), a commercially available fluorescent probe for singlet oxygen, was examined. Despite published claims to the contrary, the data presented herein indicate that SOSG can, in fact, be incorporated into a living mammalian cell. However, for a number of reasons, caution must be exercised when using SOSG. First, it is shown that the immediate product of the reaction between SOSG and singlet oxygen is, itself, an efficient singlet oxygen photosensitizer. Second, SOSG appears to efficiently bind to proteins which, in turn, can influence uptake by a cell as well as behavior in the cell. As such, incorrect use of SOSG can yield misleading data on yields of photosensitized singlet oxygen production, and can also lead to photooxygenation‐dependent adverse effects in the system being investigated.     

HovaCAL®—a generator for multi-component humid calibration gases

Process control, breath analysis for medical purpose or the investigation of biological samples are new applications of ion mobility spectrometry or differential mobility spectrometry coupled with rapid gas-chromatographic pre-separation. Especially if pre-concentration steps should be avoided, they require a realistic and flexible multi-compound calibration down to the ppt_V range including relative humidity values up to 100% for identification of analytes using mobility and retention time as well as for their quantification using the signal intensity as a measure. With HovaCAL® 3834SP-VOC, a novel calibration gas generator is presented that fulfils those requirements. The performance of HovaCAL® was validated for various compounds and mixtures with varying humidity comparing 3 particular equipments. Excellent results have been obtained with standard deviations of the provided concentrations of <8% and of <0.7% for the relative humidity range of 0–100%. Furthermore, standard deviation of the provided concentrations was <3% for varying experimental conditions. The long term stability of the provided concentrations for different instrumental parameters was proofed, standard deviations of <3% have been obtained. HovaCAL® enables for the first time a reliable calibration with complex humid mixtures down to the ppt_V range and—compared to permeation sources—a flexible and rapid change of compounds.     

2D-NMR studies of a model for Krytox® fluoropolymers

Multiple two‐dimensional nuclear magnetic resonance (2D‐NMR) techniques have been used to study the structures of Krytox^® perfluoro(polyalkyl ether) and its mechanism of polymerization. Model compound K₄, containing four Krytox^® fluoropolymer repeat units, was analyzed to interpret the multiplet patterns in the NMR spectra from the polymer model. ¹⁹F {¹³C}‐Heteronuclear single‐quantum correlation experiments, performed with delays optimized for ¹J_CF and ²J_CF, provided spectra that permitted identification of resonances from individual monomer units. Selective, ¹⁹F‐¹⁹F COSY 2D‐NMR experiments were performed with different excitation regions; these experiments were combined with selective inversion pulses to remove ¹⁹F‐¹⁹F J couplings in the f₁ dimension. The resulting COSY spectra were greatly simplified compared with standard ¹⁹F‐¹⁹F COSY spectra, which are too complicated to interpret. They give information regarding the attachments of monomer units and also provide insights into the nature of the stereoisomers that might be present in the polymer. Both infrared and NMR spectra show peaks identifying chain end structures. With the help of these studies, resonances can be assigned, and the average number of repeat units in the polymer chain can be calculated based on the assignments obtained. Copyright © 2011 John Wiley & Sons, Ltd.     

Is gluconate a good model for isosaccharinate in uranyl(VI) chemistry? A DFT study

The geometries, relative energies and spectroscopic properties of a range of α-isosaccharinate complexes of uranyl(VI) are studied computationally using ground state and time-dependent density functional theory. The effect of pH is accommodated by varying the number of water and hydroxide ligands accompanying isosaccharinate in the equatorial plane of the uranyl unit. For 1 : 1 complexes, the calculated uranyl ν(asym) stretching frequency decreases as pH increases, in agreement with previous experimental data. Three different isosaccharinate chelating modes are studied. Their relative energies are found to be pH dependent, although the energetic differences between them are not sufficient to exclude the possibility of multiple speciation. At higher pH, the uranyl-ligand interactions are dominated more by the equatorial OH(-) than by the organic ligands. Calculated electronic excitation energies support experiment in finding the lowest energy transitions to be ligand → metal charge transfer. (13)C NMR chemical shifts are calculated for the coordinated isosaccharinate in the high pH mimics, and show good agreement with experimental data, supporting the experimental conclusion that the five-membered chelate ring is favoured at high pH. The effect of increasing the isosaccharinate concentration is modelled by calculating 1 : 2 and 1 : 3 uranyl : α-isosaccharinate complexes. Comparison of the results of the present study with those from our closely related investigation of uranyl(VI)-D-gluconate complexes (Dalton Transactions 40 (2011) 11248) reveals strong similarities in structure, bonding, coordination geometry and electronic excitations, but also differences in ΔG for key ligand replacement reactions, suggesting that caution should be exercised when using gluconate as a thermodynamic model for isosaccharinate in uranyl(vi) chemistry.     

Amberlyst®-15: a reusable heterogeneous catalyst for the dehydration of tertiary alcohols

Tertiary alcohols react under mild conditions in the presence of Amberlyst^®-15 (dry) (solid-supported sulfonic acid) to give predominantly the most stable alkene in very good yield. The dehydration of tertiary alcohol functionality occurs without observation of rearrangement and polymerization products, and with outstanding substrate tolerance, which include the NHCBz, NHBoc, OSEM, OTBDMS, OBOM and ethylene ketal functional groups. Amberlyst^®-15 (dry) can be easily recovered from the reaction medium and reused for five cycles, maintaining the catalytic efficiency. In addition, the dehydration can occur under continuous operation.     

Harnessing host–guest chemistry for electrochemical sensing in complex matrices

Amid increasing demands for modernizing cumbersome and laboratory-bound analytical approaches, researchers are developing generalizable electrochemical sensing alternatives for point-of-need applications that are analogous to the glucometer. For this, integrating host–guest chemistry in electrochemical sensors represents an increasingly attractive strategy due to the vast library of host molecules and the ease with which they could be substituted for measuring different guest molecules. In response, we briefly explore the different signal transduction mechanisms (i.e., non-faradaic and faradaic) that enable electrochemical host–guest sensing. We describe the various advantages and shortcomings of the different approaches with hopes that this review will stimulate innovation toward the development of commercialized electrochemical devices relying on host–guest chemistry amenable at the point-of-need.     

Can super-resolution microscopy become a standard characterization technique for materials chemistry?

The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio–Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.

SRM, an advanced nanoscopy technique demands a transition from being a niche sophisticated technique to standard routine method for material characterization. The roadmap of necessary developments through multidisciplinary collaboration is discussed.     

Phenol solubilization in aqueous Pluronic® solutions: investigating the micellar growth and interaction as a function of Pluronic® composition

Regular one-dimensional (1D) parallel chains composed of CdS nanoparticles with cubic zinc blende crystal structure were prepared at the air/water interface via one-step synthesis and assembly process. These nanostructures were produced through an interfacial reaction between Cd(2+) ions in the aqueous solution of cadmium acetate and H(2)S in the gaseous phase under Langmuir monolayers of 10,12-pentacosadiynoic acid (PDA). It was demonstrated that PDA molecules self-assembled into parallelly aligned linear supermolecules at the air/water interface with the aid of π-π interactions and acted as templates for the formation of the superstructures. The experimental conditions including temperature and reaction time have great influences on the superstructure formation and the parameters of the parallel chains.